# State Water Resources Control Board Cases

> California Court of Appeal · February 9, 2006 · 39 Cal. Rptr. 3d 189

URL: https://www.frixlaw.com/law-library/cases/2244615

## Case

- **Full name:** State Water Resources Control Board Cases
- **Court:** California Court of Appeal
- **Decided:** February 9, 2006
- **Citations:** 39 Cal. Rptr. 3d 189; 136 Cal. App. 4th 674; 2006 Daily Journal DAR 1735; 36 Envtl. L. Rep. (Envtl. Law Inst.) 20038; 2006 Cal. Daily Op. Serv. 1218; 2006 Cal. App. LEXIS 171
- **Precedential status:** Published
- **Opinion:** Opinion by Robie
- **Judges:** Robie
- **Cited by:** 144 later opinions in the Frix Law Library

## Citator (automated)

- No negative treatment found by the automated citator. That is not the same as a confirmation that the case is good law; read the citing cases.
- Full citator and citing cases: https://www.frixlaw.com/law-library/cases/2244615

## How later opinions describe it (automated extraction)

- rejecting allegation that releases of water pursuant to D-1641 constituted waste and unreasonable use because the plaintiffs failed to demonstrate that the releases "necessarily result[] in an unreasonable use of water."
- discussing County of San Joaquin v. State Water Res. Control Bd., No. 311499 (San. Fran. Cty.Super. Ct. filed Apr. 4, 2000)

## Opinion text

Opinion
ROBIE, J.
The history of California is written on its waters—from the Eel River, to the Saltón Sea, to the Colorado River, to Lake Tahoe. But no area has been more critical than the Sacramento and San Joaquin Rivers and their great Delta and San Francisco Bay estuary.
Before us are eight appeals and three cross-appeals in seven coordinated cases known collectively as the SWRCB Cases, Judicial Council Coordinated Proceeding No. 4118. These cases arose out of an omnibus water rights proceeding before the State Water Resources Control Board (the Board) that ostensibly began with notices issued in July 1995, and ostensibly ended in March 2000 with Revised Water Right Decision 1641 (Decision 1641).
In truth, however, the water rights proceeding from which these appeals arose is but a small part of a process that has been ongoing for more than four decades to solve the problems of water quality in the San Francisco Bay/Sacramento-San Joaquin Delta Estuary.
1
In the water rights proceeding, the Board sought to allocate responsibility among various water rights holders for meeting the flow-dependent water quality objectives in the Water Quality Control Plan for the Bay-Delta, which the Board had approved in May 1995 (the 1995 Bay-Delta Plan).
2
As will be seen, Decision 1641 assigned much of that responsibility to the two great water projects in the state—the Central
*688
Valley Project (CVP), operated by the United States Bureau of Reclamation (the Bureau), and the State Water Project (SWP), operated by the Department of Water Resources (the Department)—which, in normal water years, export about 30 percent of the water that reaches the Delta. Many of the issues on appeal involve this allocation of responsibility.
The water rights proceeding giving rise to these appeals also dealt with two other long-standing issues: first, a petition filed by the Bureau and the Department in 1995 to use each other’s points of diversion in the southern Delta (the joint points of diversion petition), which had its origin in a similar petition filed by the Bureau in 1981; and second, a petition filed by the Bureau in 1985 (and thereafter amended) to change the places of use and conform the purposes of use in many of its CVP permits (the change petition).
On the joint points of diversion petition, the Board, in Decision 1641, conditionally granted the Bureau and the Department the right to use each other’s pumping plants in the southern Delta to export water to the south and west. On the change petition, the Board took two actions. Decision 1641 approved the Bureau’s request to conform the purposes of use in its CVP permits, which had the effect of adding fish and wildlife enhancement as an authorized purpose of use for water appropriated under 14 of those permits. Decision 1641 also approved the Bureau’s request to change the places of use in its CVP permits, but only in part. The Board authorized the addition of lands that were previously outside the permits’ authorized places of use but were already being served by CVP water, subject to mitigation requirements imposed on the Bureau for all of that land first converted to irrigated agricultural use by the delivery of that water. The Board did not, however, authorize the addition of lands that were not already being served by CVP water but were within the service districts of various CVP contractors. Instead, the Board determined those lands could be added later on a case-by-case basis.
Not surprisingly, given that water from the Delta is diverted to meet the needs of two-thirds of the population of California and to irrigate 4.5 million acres, many individuals and entities interested in Delta water appeared before the Board in the water rights proceeding at issue here. Again not surprisingly, not all of those parties were satisfied with the Board’s Decision 1641, which is what brings us here today. Originally, four cases challenging different aspects of the Board’s decision were coordinated and assigned to Judge Roland L. Candee. Ultimately, seven more cases were added, and three were dismissed, leaving eight.
*689
In May 2003, Judge Candee issued his statement of decision in the coordinated cases, upholding Decision 1641 with two exceptions. First, Judge Candee concluded the Board erred when it failed to allocate responsibility for meeting all of the flow objectives in the 1995 Bay-Delta Plan.
3
Second, he concluded the Board erred as to the change petition, when it refused to include all of the lands within the service area of Westlands Water District (Westlands) for authorized place of use in the Bureau’s CVP permits without any mitigation requirement. This latter conclusion rested on Judge Candee’s determination that a 1965 statute that merged Westlands with another water district
4
“effectuated a statutory authorization for the delivery of federal CVP water to all of the lands of the combined . . . district.”
From the resulting judgments, eight timely notices of appeal and three timely notices of cross-appeal were filed in seven of the coordinated cases. The Board and two other groups of parties challenge Judge Candee’s ruling that Decision 1641 failed to implement all of the flow objectives in the 1995 Bay-Delta Plan. The Board also challenges Judge Candee’s mling that it must expand the authorized place of use in the Bureau’s CVP permits to include all of the Westlands service area without any mitigation requirement. Various other parties challenge other aspects of Judge Candee’s ruling, in which he upheld the remainder of Decision 1641. These challenges raise numerous issues regarding the law of water rights, as well as issues regarding the California Environmental Quality Act (CEQA; Pub. Resources Code, § 21000 et seq.).
5
Following this introduction, we will begin by setting forth the factual and procedural background of the coordinated cases, starting with brief descriptions of the CVP and SWP and continuing with a summary of the efforts to address the problems of water quality in the Delta, which led to the Board’s adoption of the 1995 Bay-Delta Plan. From there, we will summarize the underlying water rights proceeding in which the Board sought to allocate responsibility for meeting the flow-dependent objectives in the 1995 Bay-Delta Plan among the various water rights holders with interests in water that flows into the Delta.
6
We will also describe the joint points of diversion petition and the change petition, the reasons behind those petitions, and the Board’s actions on them. We then will turn to the trial court proceedings.
*690
The discussion section of our opinion will first address arguments on appeal relating to the Board’s implementation of the 1995 Bay-Delta Plan in the water rights proceeding. We will then address challenges relating to the joint points of diversion petition. Following this, we will address challenges to the environmental impact report (EIR) the Board prepared for the implementation of the 1995 Bay-Delta Plan and for the joint points of diversion petition. After addressing challenges relating to the change petition and to the EIR the Board prepared for that petition, we will conclude by addressing challenges to the Board’s impartiality.
We agree with Judge Candee in most respects, but disagree with him in a few instances. Most significantly, we agree with Judge Candee that the Board erred when it failed to allocate responsibility for meeting all of the flow objectives in the 1995 Bay-Delta Plan. As will be seen, we conclude the Board was not entitled to implement alternate flow objectives agreed to by various interested parties in lieu of the flow objectives actually provided for in the 1995 Bay-Delta Plan. We also conclude that the Board failed to adequately implement certain salinity objectives in the 1995 Bay-Delta Plan and failed to implement the minimum flows necessary to achieve the narrative objective for salmon protection in the 1995 Bay-Delta Plan.
Unlike Judge Candee, however, we conclude the Merger Law did not impose a ministerial duty on the Board to augment the authorized place of use in the Bureau’s CVP permits to include all of the lands within the Westlands service area without mitigation. We also reject all of the alternate arguments for upholding this aspect of Judge Candee’s decision.
Based on our conclusions, we will affirm, modify, and reverse the judgments in the seven coordinated cases as appropriate.
FACTUAL AND PROCEDURAL BACKGROUND
I
The CVP and the SWP
Nearly 20 years ago, in an opinion authored by former Presiding Justice John T. Racanelli that is often identified simply as Racanelli, the Court of Appeal, First Appellate District, Division One, addressed an earlier attempt by the Board to adopt water quality objectives for the Delta.
(United States v.
*691
State Water Resources Control Bd.
(1986) 182 Cal.App.3d 82 [ 227 Cal.Rptr. 161 ].) Rather than reinvent the wheel, we will draw on that opinion extensively, particularly in setting forth the background necessary to understand the issues in these coordinated cases.
We begin with Justice Racanelli’s description of the two great California water projects—the CVP and the SWP.
A
The CVP
“The history of California water development and distribution is a story of supply and demand. California’s critical water problem is not a lack of water but uneven distribution of water resources. The state is endowed with flowing rivers, countless lakes and streams and abundant winter rains and snowfall. But while over 70 percent of the stream flow lies north of Sacramento, nearly 80 percent of the demand for water supplies originates in the southern regions of the state. And because of the semiarid climate, rainfall is at a seasonal low during the summer and fall when the demand for water is greatest; conversely, rainfall and runoff from the northern snowpacks occur in late winter and early spring when user demand is lower. [Citation.] Largely to remedy such seasonal and geographic maldistribution, while simultaneously providing relief from devastating floods and droughts, the California water projects were ultimately conceived and formed.
“In 1933 the California Legislature adopted a plan for transfer of surplus water from the Sacramento River and its northern tributaries to the water-deficient areas of the San Joaquin Valley through construction of a ‘Central Valley Project’: Shasta Dam, the central feature, to store and regulate waters of the Sacramento River; Friant Dam, on the western edge of the Sierra, to divert water from the San Joaquin River to southern regions of the valley; and various other units designed to transfer water from the Sacramento River system to the San Joaquin Valley. (Wat. Code, § 11100 et seq.) However, due to the pervasive unfavorable economic conditions during the Great Depression, the state turned to the federal government to finance and construct the massive project.
“Construction of the CVP began in 1937. It is now one of the world’s most extensive water transport systems.[
7
] As noted, Shasta Dam on the upper Sacramento River is the focal point of the CVP. Shasta Dam was completed in 1945 but began storing water and generating electric power in 1944. The
*692
waters of the Sacramento River which flow past the Shasta Dam are augmented by additional water supplies brought through a tunnel from the Trinity River and from reservoirs formed by Folsom and Nimbus Dams on the American River. About 30 miles south of Sacramento, the Delta Cross Channel regulates the passage of Sacramento River water through the Delta to the Tracy Pumping Plant.
“At Rock Slough, a portion of the water is pumped into the Contra Costa Canal for municipal uses in Contra Costa County. At the Tracy Pumping Plant, the water is lifted nearly 200 feet above sea level into the Delta[-]Mendota Canal and flows 117 miles southward to the Mendota Pool. Here, the waters from the north replace the natural flow of the San Joaquin River. At Friant Dam, the flow of the San Joaquin River is impounded and diverted through the Friant-Kem Canal 152 miles south to the southern reaches of the San Joaquin Valley.”
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at pp. 98-99, fn. omitted.)
In addition to providing water to replace the flow of the San Joaquin River at the Mendota Pool, the Delta-Mendota Canal also supplies water for agricultural users on the west side of the San Joaquin Valley and conveys water for storage in San Luis Reservoir. That reservoir provides water to CVP contractors in the San Joaquin Valley as well as to Santa Clara and San Benito Counties through the Pacheco Tunnel.
Another part of the CVP significant to this proceeding is New Melones Dam on the Stanislaus River, which joins the San Joaquin River near Vemalis. Completed in 1979, New Melones provides flood control and maintains water quality conditions in the Stanislaus and San Joaquin Rivers. Water from New Melones is also delivered to local CVP contractors.
The CVP supplies water to over 250 long-term water contractors under contracts with the Bureau. Most of those contractors put the water to agricultural use; as of 1999, CVP water was used to irrigate approximately 19,000 farms covering three million acres. The CVP also supplies water to many urban areas in Northern and Central California, including Redding, Sacramento, most of Santa Clara County, Stockton, and Fresno.
“Under section 8 of the Reclamation Act of 1902 ( 43 U.S.C. § 383 ), the . . . Bureau is required to comply with state law and to acquire water rights for diversion and storage of water by the CVP.”
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 106 ; see also
California v. United States
(1978) 438 U.S. 645 [ 57 L.Ed.2d 1018 , 98 S.Ct. 2985 ] [a state may impose any condition on control, appropriation, use or distribution of water in a federal reclamation project which is not inconsistent with clear
*693
congressional directives respecting the project].) Permit applications to appropriate water for the CVP, initially filed on behalf of the state, were assigned to the Bureau when the federal government assumed responsibility for constructing the CVP.
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 106 .) “The CVP was actually completed and in operation before permits [to appropriate water for the project] were issued; the first permits were issued to the . . . Bureau in 1958 . . . and the principal permits were issued in 1961 . . . .”
(Ibid.)
B
The SWP
“Following World War II, state authorities renewed their efforts to develop a comprehensive statewide water plan. In 1951 the Legislature authorized the Feather River and Sacramento-San Joaquin Delta Diversion Project. (§ 11260.) This project—referred to as the SWP—began operations in 1967 under management of the [Department].[
8
] Water from the Feather River is stored behind Oroville Dam and is released into the Feather River and its eventual confluence with the Sacramento River.”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at pp. 99-100, fn. omitted.) In the northern Delta, water is diverted from Barker Slough into the North Bay Aqueduct for municipal use in Solano and Napa Counties. “The water flow continues through the Delta to the Clifton Court Forebay [in the southern Delta] where a portion of it enters the South Bay Aqueduct for delivery to [urban and agricultural areas in Alameda and Santa Clara Counties], A much greater portion is lifted [at the Harvey O. Banks Delta Pumping Plant] into the [Edmund G. Brown] California Aqueduct for transport through the San Joaquin Valley [and for use by contractors in the southern San Joaquin Valley] and eventually again lifted by a series of pumping stations over the Tehachapi Mountains for delivery and use in the Southern California region.”
(Id.
at p. 100.)
SWP water is delivered to 29 long-term contractors, including agricultural users in the San Joaquin Valley, with Kern County Water Agency having the contract for the greatest amount of water. SWP water transported to Southern California is used primarily for municipal and industrial purposes; the Metropolitan Water District of Southern California is the SWP’s largest contractor.
The permits to appropriate water for operation of the SWP were issued to the Department in 1967.
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 106 .)
*694
II
Water Quality in the Delta
Obviously, the Delta plays a major role in both of California’s great water projects, as water exported by both projects to the San Francisco Bay Area, the San Joaquin Valley, and Southern California is diverted from the southern Delta for transportation to the west and south. Thus, the quality of water in the Delta is important to the projects and their contractors, as well as to other water users in and around the Delta, and to the maintenance and enhancement of fish and wildlife in the Delta.
Once again, we turn to Justice Racanelli’s opinion:
“The Delta generally describes a large lowland area with a labyrinth of natural channels in and around the confluence of the Sacramento and San Joaquin Rivers. The combined river water passes through the Delta into Suisun Bay and then into San Francisco Bay. In 1959, the legal boundaries of the Delta were fixed by the Legislature. (§ 12220.) The bounded area is roughly triangular, with Sacramento at the north, Vemalis at the south and Pittsburg at the west.
“The major factor affecting water quality in the Delta is saltwater intrusion. Delta lands, situated at or below sea level, are constantly subject to ocean tidal action. Salt water entering from San Francisco Bay extends well into the Delta, and intrusion of the saline tidal waters is checked only by the natural barrier formed by fresh water flowing out from the Delta.
“But as fresh water was increasingly diverted from the Delta for agricultural, industrial and municipal development, salinity intrusion intensified, particularly during the dry summer months and in years of low precipitation and runoff into the river systems. One of the major purposes of the projects was containment of maximum salinity intrusion into the Delta. By storing waters during periods of heavy flow and releasing water during times of low flow, the freshwater barrier could be maintained at a constant level.”
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 107 .)
*695
A
Before the 1995 Bay-Delta Plan
Efforts to address water quality problems in the Delta date back more than 40 years. In 1961, the State Water Rights Board
9
(the Water Rights Board) adopted Decision 990, which approved the Bureau’s applications for permits to appropriate water from the Sacramento River and the Delta for the CVP. In that decision, the Water Rights Board recognized the problem of salinity incursion into the Delta, but the Water Rights Board did not attach any specific water quality standards as terms and conditions of the CVP permits. Instead, the Water Rights Board reserved jurisdiction to impose such requirements later, allowing the Bureau, the state, and water users in the Delta an opportunity to reach agreement on salinity control for the Delta in the interim.
In 1965, various interested parties reached agreement on water quality criteria for the Delta—the so-called Tracy standards. (See
United States v. State Water Resources Control
Bd., supra, 182 Cal.App.3d at p. 110 .) Two years later, the Water Rights Board issued Decision 1275, which approved the Department’s applications for permits to appropriate water from the Feather River and the Delta to operate the SWP. In that decision, the Water Rights Board noted that “both federal and state agencies are conducting extensive studies regarding the problem of water quality in the San Francisco Bay and the Delta for the purpose of determining what standards of water quality should be maintained and recommending how this is to be accomplished.” Because it lacked “sufficient information ... to finally determine the terms and conditions regarding water quality in the Delta which will reasonably protect vested rights without resulting in waste of water,” the Water Rights Board reserved jurisdiction to impose terms and conditions on the SWP permits for water quality control. In the interim, the Water Rights Board limited the Department’s diversion and storage of water from April 1 through June 30 in certain circumstances and conditioned the permits on compliance with the Tracy standards.
Meanwhile, in 1966, a proposal was made to consolidate the then existing State Water Quality Control Board with the Water Rights Board into a new agency—the State Water Resources Control Board. (See generally Assem.
*696
Interim Com. on Water, A Proposed Water Resources Control Board for Cal.: A Staff Study,
supra.)
The purpose of this consolidation was “to provide for the orderly and efficient administration of the water resources of the state [by] establishing] a control board which shall exercise the adjudicatory and regulatory functions of the state in the field of water resources” and “to combine the water rights and the water pollution and water quality functions of state government to provide for consideration of water pollution and water quality, and availability of unappropriated water whenever applications for appropriation of water are granted or waste discharge requirements or water quality objectives are established.” (§ 174.) Legislation creating the consolidated Board was enacted in 1967, and the Board came into existence on December 1, 1967. (Stats. 1967, ch. 284, § 2, p. 1442.)
In 1969, the Legislature enacted a new water quality control law—the Porter-Cologne Water Quality Control Act (Porter-Cologne Act; § 13000 et seq.). (Stats. 1969, ch. 482, § 18, p. 1051; see also Robie,
Water Pollution: An Affirmative Response by the California Legislature
(1970) 1 Pacific L.J. 2.) A summary of some of the provisions of that act will assist in understanding the efforts to address water quality in the Delta that followed.
“[T]he Porter-Cologne Water Quality Control Act . . . establishes a comprehensive statewide program for water quality control administered by nine regional boards and coordinated by the state Board. The regional boards are primarily responsible for formulation and adoption of water quality control plans covering the state’s 16 planning basins (§ 13240) subject to the Board’s review and approval (§ 13245). But the Board alone is responsible for setting statewide policy concerning water quality control (§§ 13140-13147).
“And in its capacity as the designated state water pollution control agency for purposes of the Federal Water Pollution Control Act (§ 13160), the Board is empowered to formulate its own water quality control plans which supersede conflicting regional basin plans. (§ 13170.)”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 109 .)
Under the Porter-Cologne Act, “ ‘[w]ater quality control’ means the regulation of any activity or factor which may affect the quality of the waters of the state . . . .” (§ 13050, subd. (i).) “ ‘Quality of the water’ . . . refers to chemical, physical, biological, bacteriological, radiological, and other properties and characteristics of water which affect its use.”
(Id.,
subd. (g).) A water quality control plan “consists of a designation or establishment for the waters within a specified area of all of the following: [][] (1) Beneficial uses to be protected, [f] (2) Water quality objectives, [f] (3) A program of implementation needed for achieving water quality objectives.”
(Id.,
subd. (j).) “ ‘Water quality objectives’ means the limits or levels of water quality constituents or
*697
characteristics which are established for the reasonable protection of beneficial uses of water or the prevention of nuisance within a specific area.”
(Id.,
subd. (h).)
“In formulating a water quality control plan, the Board is invested with wide authority ‘to attain the highest water quality which is reasonable, considering all demands being made and to be made on those waters and the total values involved, beneficial and detrimental, economic and social, tangible and intangible.’ (§ 13000.) In fulfilling its statutory imperative, the Board is required to ‘establish such water quality objectives ... as in its judgment will ensure the reasonable protection of beneficial uses . . .’ (§ 13241), a conceptual classification far-reaching in scope.[
10
] ‘ “Beneficial uses” of the waters of the state that may be protected against quality degradation include, but are not necessarily limited to, domestic, municipal, agricultural and industrial supply; power generation; recreation; aesthetic enjoyment; navigation; and preservation and enhancement of fish, wildlife, and other aquatic resources or preserves.’ (§ 13050, subd. (f).) Thus, in carrying out its water quality planning function, the Board possesses broad powers and responsibilities in setting water quality [objectives].”
11
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at pp. 109-110.)
The program of implementation that must be included in every water quality control plan must “include, but not be limited to: [][] (a) A description of the nature of actions which are necessary to achieve the objectives, including recommendations for appropriate action by any entity, public or private. [][] (b) A time schedule for the actions to be taken, [f] (c) A description of surveillance to be undertaken to determine compliance with objectives.” (§ 13242.) Also, the Board may “not adopt any water quality control plan unless a public hearing is first held, after the giving of notice . . . .” (§ 13244.)
“In performing its regulatory function of ensuring water quality by establishing water quality objectives, the Board acts in a legislative capacity.”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 112 .) “[W]ater quality control plans ... are quasi-legislative.”
(State Water Resources Control Bd. v. Office of Admin. Law
(1993) 12 Cal.App.4th 697, 701-702 [ 16 Cal.Rptr.2d 25 ].)
*698
In 1971, following the enactment of the Porter-Cologne Act, “the Board issued Decision 1379 establishing new water quality [objectives] purportedly applicable to both the CVP and the SWP. The decision was stayed as a result of litigation challenging the Board’s authority to impose conditions on permits held by a federal agency.[
12
]
“At about the same time, the regional water quality control boards (see § 13240) formulated plans for the 16 ‘basins’ of the state, including the Delta and the Suisun Marsh. The Basin 5B Plan, setting water quality [objectives] for the Delta, and the Basin 2 Plan, setting [objectives] for the San Francisco Bay Basin, were finally approved by the Board in 1975.
“In approving the Basin 5B Plan, the Board indicated its intention to convene hearings no later than July 1, 1978, for the purpose of receiving further evidence relating to salinity control and protection of fish and wildlife. [Over an 11-month period], the Board held an extended evidentiary hearing culminating in [August 1978 with the] adoption of the 1978 Water Quality Control Plan for the Sacramento-San Joaquin Delta and Suisun Marsh. The Plan [wa]s intended to remain in effect for 10 years with new hearings to be scheduled in 1986 to reevaluate the Delta [objectives],
“In conducting the 1978 proceedings, the Board for the first time acted pursuant to its combined authority to determine water rights and to establish water quality [objectives]. (§ 174.) In discharging its dual functions, the Board reconsidered existing water quality [objectives] in light of current data concerning the effects on the Delta of the operations of the two water projects—the users with the greatest impact. The Board also undertook to modify the existing water rights permits of the projects—the water rights holders with the lowest seniority—in order to implement the enacted water quality [objectives].
“The final product of the Board’s efforts was the Water Quality Control Plan for the Sacramento-San Joaquin Delta and Suisun Marsh and Water Right Decision 1485. In the Plan, the Board set new water quality [objectives] to protect fish and wildlife and to protect agricultural, industrial and municipal uses of Delta waters. In the Decision, the Board modified the permits held by the . . . Bureau and the [Department] to compel the projects to release enough water into the Delta or to reduce their exports from the Delta so as to maintain the water quality [objectives] set in the Plan.”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at pp. 110-111.)
A number of parties filed mandamus petitions seeking to invalidate the water quality control plan and Decision 1485.
(United States v. State Water
*699
Resources Control Bd., supra,
182 Cal.App.3d at p. 111 .) In the coordinated proceeding on those petitions, the trial court rejected the Board’s water quality objectives as inadequate and issued a writ of mandate commanding the Board to set aside the plan and the decision and to reconsider the plan.
(Id.
at pp. 111, 120.)
On appeal, in the 1986 opinion authored by Justice Racanelli, the appellate court concluded “that the modification of the projects’ permits in order to implement the water quality [objectives] was a proper exercise of the Board’s water rights authority,” but “in establishing only such water quality [objectives] as will protect Delta water users against the effects of project activities, the Board misconceived the scope of its water quality planning function.”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 98 .) According to the court, “the Board has the power and duty to provide water quality protection to the fish and wildlife that make up the delicate ecosystem within the Delta.”
(Ibid.)
The appellate court also concluded that “the procedure followed—combining the water quality and water rights functions in a single proceeding—was unwise” because in doing so “the Board compromised its important water quality role by defining its scope too narrowly in terms of enforceable water rights.”
(Id.
at pp. 119, 120.)
Because the Board had already announced its “intention to conduct hearings during 1986 to establish new and revised” water quality objectives, the appellate court determined that “remand to the Board could serve no useful purpose.”
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 120 .) Accordingly, the court reversed the judgment commanding the Board to reconsider the water quality control plan and instead simply expressed its expectation that “the renewed proceedings [would] be conducted in light of the principles and views expressed in [the court’s] opinion.”
(Ibid.)
As a result, Decision 1485 remained in effect.
A description of the next phase in the history of water quality control in the Delta can be found in the 1995 Bay-Delta Plan:
“In July 1987, the [Board] began proceedings to reexamine water quality objectives for the Bay-Delta Estuary and consider how water right permits would be modified to meet the new objectives. In May 1991, the [Board] adopted the 1991 Bay-Delta Plan with objectives for salinity, dissolved oxygen, and temperature. The 1991 Bay-Delta Plan was subsequently submitted to the U.S. Environmental Protection Agency (USEPA) for approval. In September 1991, the USEPA approved all of the salinity objectives for municipal, industrial, and agricultural beneficial uses, and the dissolved oxygen objective for fish and wildlife beneficial uses. The USEPA stated that the other fish and wildlife objectives were disapproved because of their
*700
failure to protect estuarine habitat and other fish and wildlife beneficial uses. As required under federal regulations [citation] when a state does not adopt changes in standards recommended by the USEPA upon notification of approval or disapproval of a state’s standards, the USEPA initiated promulgation of water quality standards for the Bay-Delta Estuary. In January 1994, the USEPA published draft standards for the Estuary in the Federal Register [citation].
“To coordinate the parallel State and federal Bay-Delta resource management activities, the Governor’s Water Policy Council of the State of California (Council) and the Federal Ecosystem Directorate (FED), comprised of State and federal resource agencies collectively known as CALFED, entered into a Framework Agreement in June 1994. The purpose of the agreement is to establish a comprehensive program for coordination and communication between the Council and the FED regarding environmental protection and water supply dependability in the Bay-Delta Estuary and its watershed. The CALFED agreement identifies three areas where both State and federal interests and responsibilities are interrelated, and coordination and cooperation are particularly important: (1) formulation of water quality standards for the Estuary; (2) improved coordination of federal and State water project operations with regulatory requirements; and (3) development of a long-term solution to fish and wildlife, water supply reliability, flood control, and water quality problems in the Bay-Delta Estuary. In accordance with the Framework Agreement, the administrator of the USEPA signed final federal standards for the Estuary on December 14, 1994.” (1995 Bay-Delta Plan, pp. 5-6, fn. omitted.)
Meanwhile, in March 1994, the Board commenced a proceeding to revise the water quality objectives for the Bay-Delta. During public workshops, the Board encouraged interested parties to develop alternatives for revising the objectives. Eventually, various representatives of the state and federal governments and certain urban, agricultural, and environmental interests reached agreement on recommendations to the Board for the revised objectives. This agreement is embodied in a document entitled “Principles for Agreement on Bay-Delta Standards between the State of California and the Federal Government” (principles for agreement), which was signed on December 15, 1994. Among the signatories were the Secretary of the California Resources Agency and the Secretary for the California Environmental Protection Agency.
The same day the principles for agreement were signed, the Board released the first draft of its new water quality control plan for the Bay-Delta. The Board used several elements of the principles for agreement, as well other recommendations from interested parties, in preparing the draft plan.
*701
B
The 1995 Bay-Delta Water Quality Control Plan
The Board adopted the new water quality control plan for the Bay-Delta in May 1995. The 1995 Bay-Delta Plan identified 17 beneficial uses, both within the Delta and throughout the state, to be served by the waters of the Delta. These uses fall into three broad categories: municipal and industrial, agricultural, and fish and wildlife. The 1995 Bay-Delta Plan then identified water quality objectives with respect to each of these categories of uses “to attain the highest water quality which is reasonable, considering all demands being made on the waters of the Estuary.” (1995 Bay-Delta Plan, p. 14.) The Board established various salinity objectives “for the reasonable protection of [agriculture as a beneficial use] from the effects of salinity intrusion and agricultural drainage in the western, interior, and southern Delta.” To protect fish and wildlife uses, the Board’s plan established objectives for six parameters: dissolved oxygen, salinity, amounts of Delta outflow, river flows, export limits, and Delta cross-channel gate operation. The plan also included a narrative objective for salmon protection. The objectives at issue in these coordinated cases are described below.
1.
The Southern Delta Salinity Objectives
The Board adopted various salinity objectives in the plan (expressed as electrical conductivity or EC) to protect agricultural uses in the western, interior, and southern Delta. To protect agricultural uses in the southern Delta, the Board adopted salinity objectives to be met at four different locations: (1) San Joaquin River at Airport Way Bridge, Vemalis (the Vemalis salinity objective); (2) San Joaquin River at Brandt Bridge; (3) Old River near Middle River; and (4) Old River at Tracy Road Bridge. The 1995 Bay-Delta Plan specified the objectives as 0.7 EC from April through August and 1.0 EC from September through March at all four locations, but specified in a footnote that the objectives were to be met at the two Old River locations by December 31, 1997. (1995 Bay-Delta Plan, p. 17.)
2.
The Delta Outflow Objective
Water flow can be regulated as a water quality objective because, as the Board explained in the 1995 Bay-Delta Plan, “the rate and quantity of flow ... are physical properties or characteristics of the water” which “have an impact on the beneficial uses of’ water in the Bay-Delta. (See § 13050, subd. (g).) Thus, a flow objective sets the amount of water that must be flowing in a watercourse at a given time “for the reasonable protection of beneficial uses of [the] water.”
(Id.,
subd. (h).) Obviously, meeting such an
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objective may be achieved, among other ways, by reducing the amount of water that upstream water right holders divert from the watercourse or by increasing the amount of water released into the watercourse.
In the 1995 Bay-Delta Plan, the Board explained that “Delta outflow objectives are included for the protection of estuarine habitat for anadromous fishes and other estuarine-dependent species.” The parameter for those objectives was the net Delta outflow index (outflow index). The outflow index was a number representing the net amount of water flowing out of the Delta, which was to be calculated by talcing the amount of water flowing into the Delta and subtracting from that figure the amount of water being consumed in the Delta and the amount of water being exported from the Delta. For example, every year in September, the 1995 Bay-Delta Plan required a minimum monthly average outflow index of 3,000 cubic feet per second (cfs) of water to be flowing out of the Delta to protect estuarine habitat within the Delta. (1995 Bay-Delta Plan, pp. 15, 19, 25.)
3.
The Vernalis Flow Objectives
As part of the river flow objectives in the 1995 Bay-Delta Plan, the Board set minimum monthly average flow rates on the San Joaquin River at Vernalis (the Vernalis flow objectives). The Board explained that “Sacramento and San Joaquin river flow objectives are included to provide attraction and transport flows and suitable habitat for various life stages of aquatic organisms, including Delta smelt and chinook salmon.” One part of the Vernalis flow objectives was a “pulse” flow during a 31-day period in April and May of each year (the Vernalis pulse flow objective). The 1995 Bay-Delta Plan called for an average flow rate during that period ranging from 3,110 to 8,620 cfs, depending on the type of water year and on certain salinity measurements.
13
The 1995 Bay-Delta Plan also specified that while the default period for the pulse flow was April 15 to May 15, “[t]his time period may be varied based on real-time monitoring. One pulse, or two separate pulses of combined duration equal to the single pulse, should be scheduled to coincide with fish migration in San Joaquin River tributaries and the Delta. The time period for this 31-day flow requirement will be determined by the operations group established under the Framework Agreement.” (1995 Bay-Delta Plan, p. 21, table " " . [18].)
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4.
The Salmon Protection Objective
The 1995 Bay-Delta Plan also included a narrative objective for the protection of salmon, which provided: “Water quality conditions shall be maintained, together with [other] measures in the watershed, sufficient to achieve a doubling of natural production of chinook salmon from the average production of 1967-1991, consistent with the provisions of State and federal law.” (1995 Bay-Delta Plan, p. 18, table 3.)
5.
The Program of Implementation
In addressing implementation of the objectives in the 1995 Bay-Delta Plan, the Board divided the program of implementation into “four general components: (1) measures within [the Board’s] authority over water diversion and use which implement the water quality objectives; (2) measures requiring a combination of [the Board’s] water quality and water rights authorities and actions by other agencies to implement the objectives; (3) recommendations to other agencies to improve fish and wildlife habitat conditions; and (4) a monitoring and special studies program.” The Board then explained: “The specific actions identified within these components include time schedules for implementation, if appropriate. If no time schedule is included, implementation should be immediate.” (1995 Bay-Delta Plan, p. 27.)
The Board included within the first component of its program of implementation the agricultural salinity objectives (with the exception of those for the protection of the southern Delta), the Delta outflow objectives, and the river flow objectives for the protection of fish and wildlife, including the Vemalis pulse flow objective. In describing “the nature of [the] actions . . . necessary to achieve the[se] objectives” (§ 13242, subd. (a)), the Board explained that it would “initiate a water rights proceeding following adoption of this water quality control plan” that would “address the water supply-related objectives in this plan through the amendment of water rights under the authority of the [Board].” According to the Board, “[t]he water right decision . . . will allocate responsibility for meeting the objectives among water rights holders in the Bay-Delta Estuary watershed and establish terms and conditions in appropriate water rights.” The Board noted that pending adoption of that decision, which the Board anticipated would occur before June 1998, “the [Bureau] intends to meet San Joaquin River flow requirements, in accordance with the March 6, 1995 U.S. Fish and Wildlife Service (USFWS) biological opinion for the threatened Delta smelt, which are consistent with the San Joaquin River flow objectives in this plan. These flows are interim flows and will be reevaluated as to timing and magnitude, up or down, within the next three years. During the three-year period, decisions by the FERC [the Federal Energy Regulatory Commission] or other regulatory
*704
orders may increase flows to the Estuary required of upstream water users. These flows will be considered by the [Board] in its allocation of responsibility among the water rights holders in the watershed during the water rights proceeding.” (1995 Bay-Delta Plan, p. 29.)
The Board included within the second component of the program of implementation—“measures requiring a combination of [the Board’s] water quality and water rights authorities and actions by other agencies to implement the objectives”—the agricultural salinity objectives for the southern Delta, including the Vemalis salinity objective. The Board explained: “Elevated salinity in the southern Delta is caused by low flows, salts imported in irrigation water by the State and federal water projects, and discharges of land-derived salts, primarily from agricultural drainage. Implementation of the objectives will be accomplished through the release of adequate flows to the San Joaquin River and control of saline agricultural drainage to the San Joaquin River and its tributaries. Implementation of the agricultural salinity objectives for the two Old River sites shall be phased in so that compliance with the objectives is achieved by December 31, 1997.” (1995 Bay-Delta Plan, pp. 27, 29.)
With respect to the Vemalis salinity objective in particular, the Board explained: “This plan’s objectives, for flows in the San Joaquin River at Vemalis are expected to contribute to achieving the salinity objectives in the southern Delta. Presently, the [Bureau] is responsible for meeting Vemalis salinity objectives through the release of water from New Melones Reservoir, as required under Water Right Decision 1422. Additional releases from other reservoirs for fish and wildlife protection in San Joaquin River tributaries may be required through ongoing FERC proceedings. Implementation of the [Board]’s Nonpoint Source Management Plan, adopted in 1988, and recommended activities of the multi-agency San Joaquin Valley Drainage Program (SJVDP), discussed below, will also contribute to achieving the salinity objectives. Additionally, the Central Valley [Regional Water Quality Control Board] should continue its salt load reduction program, initiated in response to adoption of the 1991 Bay-Delta Plan, to reduce annual salt loads discharged to the San Joaquin River by at least 10 percent and to adjust the timing of such discharges from low flow to high flow periods. These source control and drainage management measures will decrease the need for releases of water from New Melones. The [Board] will evaluate implementation measures for the southern Delta agricultural salinity objectives in the water rights proceeding.” (1995 Bay-Delta Plan, p. 29.)
The plan also included, in the second component of the program of implementation, the narrative objective for salmon protection. The Board explained: “It is uncertain whether implementation of the numeric objectives
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in this plan alone will result in achieving the narrative objective for salmon protection. Therefore, in addition to the timely completion of a water rights proceeding to implement river flow and operational requirements which will help protect salmon migration through the Bay-Delta Estuary, other measures may be necessary to achieve the objective of doubling the natural production of chinook salmon from average 1967-1991 levels. This narrative objective is consistent with the anadromous fish doubling goals of the [CVP Improvement Act]; thus, prompt and efficient actions taken to implement this [CVP Improvement Act] goal, in concert with other recommended actions in this plan, are important to achieving the narrative salmon protection objective. Monitoring results will be considered in the ongoing review to evaluate achievement of this objective and the development of numeric objectives to replace it.” (1995 Bay-Delta Plan, pp. 28-29.)
In discussing the third component of the program of implementation— “recommendations to other agencies to improve fish and wildlife habitat conditions”—the plan recommended the development of “an experimental study program on the effects of pulse flows on fish eggs and larvae in the Delta.” More specifically, the Board stated: “The [Department] and the [Bureau] should conduct experiments to investigate and evaluate the biological benefits of pulse flows to move planktonic fish eggs and larvae into Suisun Bay. These experiments, which should be conducted as soon as feasible, should: (1) involve flows released from both the Sacramento and San Joaquin rivers; (2) include real-time biological monitoring to determine the most favorable times for the pulse flows and the effects of the pulse flows on the eggs and larvae; (3) determine whether short-term pulse flows have a lasting benefit or whether, when outflows are reduced after a pulse flow, the larval fish are drawn back into interior Delta areas; and (4) take into account base flows and availability of water supplies. If results of the experiments were obtained soon enough, they could be used to refine potential pulse flow requirements in a water right decision implementing this water quality control plan.” (1995 Bay-Delta Plan, p. 38.)
C
The Water Rights Proceeding to Implement the 1995 Bay-Delta Plan
In November 1997, the Board issued a draft environmental impact report for implementation of the 1995 Bay-Delta Plan (the implementation EIR). The following month, the Board issued a notice of public hearing, setting hearing dates for the water rights proceeding in which the Board would allocate responsibility for implementing the flow-dependent objectives of the
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1995 Bay-Delta Plan. (As discussed more fully below, this water rights proceeding also encompassed the petitions by the Bureau and the Department for certain changes in their CVP and SWP permits.)
Ultimately, the Board divided the public hearing into eight phases. The hearing convened on July 1, 1998, and continued off and on until July 6, 1999. On December 29, 1999, the Board certified the final implementation EIR and issued Decision 1641. On March 15, 2000, following the filing of various petitions for reconsideration, the Board issued its order denying petitions for reconsideration and amending Decision 1641 (order on reconsideration) and issued the revised decision that we refer to as Decision 1641. ( (as of Feb. 9, 2006).) With respect to its allocation of responsibility for meeting the flow-dependent objectives in the 1995 Bay-Delta Plan, we describe the most pertinent parts of Decision 1641 below.
1.
Responsibility for Meeting the Vernalis Flow Objectives—The San Joaquin River Agreement and the Vernalis Adaptive Management Plan
In a revised notice of public hearing issued in May 1998, the Board explained that “[sjeveral agreements have been negotiated among the parties interested in this proceeding, proposing allocations of responsibility to meet the flow-dependent objectives in the 1995 Bay-Delta Plan. The [Board] will receive evidence on these agreements during the hearing and will consider adopting water right terms and conditions consistent with these agreements.” One such agreement was the proposed San Joaquin River Agreement—an agreement between “some, but not all, of the parties who have an interest in the allocation of responsibility to provide the San Joaquin River’s share of water for meeting the Bay-Delta flow objectives.”
14
(Decision 1641, p. 18.)
As the Board explained in Decision 1641: “The [San Joaquin River Agreement] was presented to the [Board] as a settlement agreement proposing an allocation of responsibility for meeting the April-May objective for pulse flows from the San Joaquin River.” “For a twelve-year period, the [San Joaquin River Agreement] proposes to allocate responsibility for meeting the April-May pulse flow objectives in the 1995 Bay-Delta Plan to certain water
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right holders in the watershed of the San Joaquin River.” Under the San Joaquin River Agreement, “[t]he members of the [San Joaquin River Group Authority] who provide the water will receive $3 million per year from the [Bureau], . . . and $1 million per year from the [Department]... . . The [San Joaquin River Agreement] would assign responsibility to the [Department] and the [Bureau] to meet the flows it specifies during the pulse flow period in the southern Delta.” (Decision 1641, pp. 12, 17, 18.) In addition, “[t]he [Department] and the [Bureau] have committed themselves to provide ‘backup’ during the term of the [San Joaquin River Agreement] for any responsibility that otherwise would be placed on the San Joaquin basin water right holders as a result of an allocation of responsibility in the Bay-Delta Water Rights Hearing.”
15
(Id.,
p. 18, fn. 26.)
The San Joaquin River Agreement, however, did not provide sufficient flows to meet all of the Vemalis flow objectives in the 1995 Bay-Delta Plan. Nevertheless, to induce the Board to approve the San Joaquin River Agreement as part of Decision 1641, the Bureau and the Department committed to provide additional water, beyond what was required by the agreement, to meet all of the Vemalis flow objectives
except
the Vemalis pulse flow objective.
The reason the parties to the San Joaquin River Agreement were not proposing to meet the Vemalis pulse flow objective was ostensibly to conduct an experiment known as the Vemalis Adaptive Management Plan, which had been developed “to gather better scientific fisheries information on the lower San Joaquin River”—specifically, “information on the relative effects of flows in the San Joaquin River, CVP and SWP pumping rates, and operation of a fish barrier at the head of Old River on the survival and passage of salmon smolts through the Delta.” According to the San Joaquin River Agreement, the flows and pumping regimen provided for in the agreement would not only allow the conduct of the Vemalis Adaptive Management Plan but would “provide environmental benefits in the lower San Joaquin River and Delta at a level of protection equivalent to the San Joaquin River Portion of the” 1995 Bay-Delta Plan. (San Joaquin River Agreement, § 2.1.)
To implement the San Joaquin River Agreement, four petitions were filed for long-term changes in licenses held by Merced, Turlock, Modesto,
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Oakdale, and South San Joaquin Irrigation Districts (the irrigation districts).
16
The petitions proposed to add the San Joaquin River upstream of Vemalis as a place of use and add fish and wildlife enhancement as a purpose of use. These changes would allow these irrigation districts to contribute water toward the Vemalis pulse flow.
As Decision 1641 explained: “Pursuant to the [San Joaquin River Agreement], [the irrigation districts] along with the [San Joaquin River Exchange Contractors Water Authority] would provide up to 110 taf [thousand acre-feet] per year during a 31-day pulse flow period in April and May of each year, for instream flows in the lower San Joaquin River above Vemalis. . . . The [irrigation districts] and the Exchange Contractors would decide each year how to allocate the water required during the pulse flow period.” (Decision 1641, p. 14, fn. omitted.)
In evaluating the Vemalis Adaptive Management Plan, the Board concluded it provided “a unique opportunity for collecting data under controlled conditions because of the commitment of the [Department] and [the Bureau] to control exports and releases from New Melones Reservoir, and operate the head of Old River barrier as needed for the experiment.” (Decision 1641, p. 21.) The Board also noted, however, that “[t]here are differences in the flow targets between the [Vemalis Adaptive Management Plan] and the [San Joaquin River Agreement],” and “the [San Joaquin River Agreement] does not fully provide for conducting the experiment as designed.”
(Id.,
pp. 20, 22.) Among other things, “the [San Joaquin River Agreement] provides flow targets of 2,000 cfs, but the minimum flow targets under the [Vemalis Adaptive Management Plan] are 3,200 cfs.”
(Id.,
p. 20, fn. omitted.) The Board “urges the [Bureau] to supplement the flows provided under the [San Joaquin River Agreement] as needed to ensure that the experiment is completed,” but the Board did not require the Bureau to do so.
(Id.,
p. 22.)
In evaluating the San Joaquin River Agreement, the Board declined a request by its proponents to find that the agreement provided environmental protection equivalent to the Vemalis pulse flow objective in the 1995 Bay-Delta Plan. According to the Board: “A finding of equivalent protection would be premature at this time. The purpose of the [San Joaquin River Agreement] and [the Vemalis Adaptive Management Plan] is to determine through experimentation alternative measures to protect the beneficial uses in the 1995 Bay-Delta Plan designated to be protected by the Vemalis pulse flow
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objectives. Until the experiment is complete, there will not be adequate information to know whether the measures provide equivalent protection.” (Decision 1641, p. 23.)
The Board went on to note that “the Vemalis flow objectives in the 1995 Bay-Delta Plan do not contain a provision allowing a different set of objectives to be met if it is demonstrated that they provide equivalent protection for the beneficial uses protected by the objectives. In cases where equivalent protection can be provided, the objectives normally so state. Instead of providing for equivalent protection, the 1995 Bay-Delta Plan provides that the Vemalis flow objectives will be reevaluated in a future review of the plan.” (Decision 1641, p. 23.)
The Board candidly acknowledged that “[mjeeting the flows specified in the [Vemalis Adaptive Management Plan] will not meet the pulse flow objectives” in the 1995 Bay-Delta Plan and “it is not certain that the [Vemalis Adaptive Management Plan] will provide protection for the Chinook salmon equivalent to that provided by the objectives.” Nonetheless, the Board “approves the [San Joaquin River Agreement] for the purpose of conducting the [Vemalis Adaptive Management Plan] experiment” on the theory that “[ujnder Water Code section 13242, an objective can be implemented in stages over a period of time” and “[t]he [Vemalis Adaptive Management Plan] experiment . . . will serve as a step toward implementation of the Vemalis pulse flow objectives.” According to the Board, by approving the agreement, it was “authorizing] a staged implementation of the Vemalis pulse flow objectives so that experimental operations can be conducted in lieu of meeting the objectives as the first stage of implementation.” (Decision 1641, pp. 23, 24, 48.)
To allow for performance of the San Joaquin River Agreement, the Board in Decision 1641 amended two of the Bureau’s permits for New Melones storage to require the Bureau to meet the Vemalis flow objectives during the term of the agreement, with the exception of the Vemalis pulse flow objective. In lieu of the Vemalis pulse flow objective, the Bureau was required to meet the alternate pulse flow objectives from the agreement. The Board specifically explained that this was an interim requirement and that it would “consider a permanent allocation of responsibility with respect to the San Joaquin River basin after the [San Joaquin River Agreement] has expired.” The new permit term provided that “[i]f the San Joaquin River Agreement ... is dissolved by the signatory parties before it expires, then Permittee shall meet the San Joaquin River flow objective set forth in [the 1995 Bay-Delta Plan] until the Board establishes alternative implementation of the San Joaquin River flow objective.” (Decision 1641, pp. 132, 162.) The Board also explained that the Bureau was not required to “use water under
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[the New Melones] permits to meet [the Vemalis flow objectives] if it uses other sources of water or other means to meet these” objectives.
(Id.,
p. 160, fit. 87.)
The Board also approved the petitions by the irrigation districts to add the San Joaquin River upstream of Vemalis as a place of use and add fish and wildlife enhancement as a purpose of use in their licenses during the period of the San Joaquin River Agreement. Consistent with the terms of the San Joaquin River Agreement, the Board required the irrigation districts to contribute up to 110 thousand acre-feet (taf) of water annually toward the alternate pulse flow objectives from the agreement. The Board further specified that “[w]hen the [San Joaquin River Agreement] expires or is terminated, the Board will give notice and will commence a proceeding to determine the responsibility of the [irrigation districts] to meet the objectives.” (Decision 1641, p. 166.)
2.
Responsibility for Meeting the Southern Delta Salinity Objectives
In Decision 1641, the Board determined that salinity concentrations at Vemalis are caused by “a combination of upstream water diversions, discharges of saline drainage water to the San Joaquin River and subsurface accretions to the river from groundwater.” The Board further determined “that the actions of the CVP are the principal cause of the salinity concentrations exceeding the objectives at Vemalis.” This is so because “[t]he source of much of the saline discharge to the San Joaquin River is from lands on the west side of the San Joaquin Valley which are irrigated with water provided from the Delta by the CVP,” and “[t]he capacity of the lower San Joaquin River to assimilate the agricultural drainage has been significantly reduced through the diversion of high quality flows from the upper San Joaquin River by the CVP at Friant.” (Decision 1641, pp. 80, 83.)
Because the Board viewed the CVP as the cause of the salinity concentration at Vemalis, the Board required the Bureau to meet the Vemalis salinity objective. The Board specified that the Bureau would have “wide latitude in developing a program to achieve this result” and “could consider sources of dilution water other than New Melones Reservoir and other means of reducing the salinity concentration in the southern Delta.” To this end, the Board inserted a condition in all of the Bureau’s CVP permits, except those relating to New Melones, which “conditioned [those permits] on implementation of the water quality objectives for agricultural beneficial uses in the southern Delta,” including the Vemalis salinity objective. This condition specified that the Bureau could meet the Vemalis salinity objective “through flows or other measures.”
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The Board added a term to the two New Melones storage permits, which provided that “[i]n conjunction with other measures to control salinity, Permittee shall release water from New Melones Reservoir to maintain the Vemalis agricultural salinity objective.” The Board added a condition to the New Melones direct diversion permit which provided that “[f]or the protection of water quality, no diversion is authorized for consumptive uses under this permit unless [the Vemalis salinity objective] is met. ...” In all three of these New Melones permits, Decision 1641 specified that the Bureau could “meet these objectives through flows or other measures.” In addition, in the two New Melones storage permits, the Board provided that the Bureau did not have to “use water under these permits to meet [the Vemalis salinity objective] if it uses other sources of water or other means.” (Decision 1641, pp. 160 & fn. 87, 161, 162.)
With respect to the three other agricultural salinity objectives for the southern Delta downstream of Vemalis, the Board determined the Department and the Bureau were partially responsible for the salinity problems at those locations because of export pumping. Decision 1641 noted that “[m]easures that affect circulation in the Delta, such as barriers, can help improve the[se] salinity concentrations” (Decision 1641, p. 89) and that the Department and the Bureau were working together on a barrier program. The Board amended all of the Department’s SWP permits and all of the Bureau’s CVP permits to require the Department and the Bureau to implement the salinity objectives at the three locations. The Board, however, did not require immediate implementation of the 0.7 EC objective for April through August at any of the three locations. Instead, in a revision to the footnote in the 1995 Bay-Delta Plan that previously allowed the salinity objectives at the two Old River locations to be implemented by December 31, 1997, the Board now specified that at all three locations the 0.7 EC objective “becomes effective on April 1, 2005” (Decision 1641, p. 182, table 2, fn. [5]) and that the Department and the Bureau were to meet the 1.0 EC objective year round until that date. The Board further specified: “The 0.7 EC objective is replaced by the 1.0 EC objective from April through August after April 1, 2005 if permanent barriers are constructed, or equivalent measures are implemented, in the southern Delta and an operations plan that reasonably protects southern Delta agriculture is prepared by the [Department] and the [Bureau] and approved by the Executive Director of the [Board], The [Board] will review the salinity objectives for the southern Delta in the next review of the Bay-Delta objectives following construction of the barriers.”
(Ibid.)
3.
Responsibility for Meeting the Delta Outflow Objective
The Board assigned responsibility for meeting the Delta outflow objective to both the Bureau and the Department by adding a term to all of the CVP
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and SWP licenses and permits, requiring the Bureau and the Department to ensure that the Delta outflow objective was met “on an interim basis . . . until the Board adopts a further decision in the Bay-Delta Water Rights Hearing assigning responsibility for meeting these objectives.”
17
Ill
The Joint Points of Diversion Petition and the Change Petition
In addition to allocating responsibility for meeting the flow-dependent objectives in the 1995 Bay-Delta Plan, the Board used the public hearing held between July 1998 and July 1999 to consider petitions by the Department and the Bureau for certain changes in their water right permits. To better understand the issues raised by those petitions, a brief review of California law on the appropriation of water is necessary.
To acquire the right to appropriate water, “an application for appropriative rights must... be made to the Board for a permit authorizing construction of necessary water works and the taking and use of a specified quantity of water.”
(United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 102 .) Among other things, an application for a permit to appropriate water must include “[t]he nature and amount of the proposed use,” “[t]he proposed place of diversion,” and “[t]he place where it is intended to use the water.” (§ 1260, subds. (c), (e), (f).)
The Board “shall allow the appropriation for beneficial purposes of unappropriated water under such terms and conditions as in its judgment will best develop, conserve, and utilize in the public interest the water sought to be appropriated.” (§ 1253.) “The issuance of a permit gives the right to take and use water only to the extent and for the purpose allowed in the permit.” (§ 1381.) “Water appropriated ... for one specific purpose shall not be deemed to be appropriated for any other or different purpose, but the purpose of the use of such water may be changed as provided in [the Water C]ode.” (§ 1700.)
“At any time after notice of an application is given, an applicant, permittee, or licensee may change the point of diversion, place of use, or purpose of use from that specified in the application, permit, or license; but such change may be made only upon permission of the board.” (§ 1701.) “Before permission to
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make such a change is granted the petitioner shall establish, to the satisfaction of the board, and it shall find, that the change will not operate to the injury of any legal user of the water involved.” (§ 1702.)
With that legal framework in mind, we turn to the petitions at issue here.
A
The Joint Points of Diversion Petition
In the late 1970’s and early 1980’s, the Bureau filed petitions for temporary use of the SWP’s pumping plant in the southern Delta to take advantage of excess capacity at that plant. In Decision 1485, which the Board implemented in 1979 (and which remained in effect through the adoption of Decision 1641), the Board authorized the Bureau to use the SWP’s pumping plant to make up export deficiencies caused by limits imposed on the Bureau’s pumping plant in May and June of each year for the protection of striped bass.
In December 1981, the Bureau filed a petition for the permanent right to use the SWP’s pumping plant. In 1985, the Bureau renewed this request in its petition to consolidate and expand the places of use in 15 of its CVP permits (discussed more fully below). Finally, in February 1995, the Bureau and the Department filed with the Board a petition to add to the permits for the CVP and the SWP “points of diversion and rediversion at each project’s diversion facilities in the southern Delta to allow the projects to use those facilities interchangeably” (the joint points of diversion petition). Specifically, the Bureau sought to add the SWP’s Harvey O. Banks Delta Pumping Plant as a point of diversion and rediversion in the permits for the CVP, and the Department sought to add the CVP’s Tracy Pumping Plant as a point of diversion and rediversion in the permits for the SWP.
In the water rights proceeding underlying these coordinated cases, the Board addressed the requests for joint points of diversion made in 1981, 1985, and 1995. The draft implementation EIR issued by the Board in November 1997 included an analysis of the potential environmental impacts of granting the joint points of diversion petition. The revised notice of public hearing issued by the Board in May 1998 gave notice that phase 6 of the hearing would address the joint points of diversion petition.
The Board received evidence regarding the joint points of diversion petition over seven days in May 1999. As previously noted, the Board certified the implementation EIR on December 29, 1999. In Decision 1641, the Board approved the joint points of diversion petition in three stages,
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imposing “[operations plans and other requirements ... on changes in use of the [joint points of diversion] from one stage to the next. The operations plan must be protective of fish and wildlife and of the rights of other legal users of the water. It will be subject to the approval of the Chief of the Division of Water Rights of the [Board]. With these requirements, the [joint points of diversion] will not cause injury to other legal users of the water, and will not have a significant effect on the environment.” (Decision 1641, p. 91.)
B
The Change Petition
In September 1985, the Bureau filed a petition with the Board to consolidate and expand the places of use in 15 of its CVP permits (the change petition). In its petition, the Bureau offered the following explanation for the expansion aspect of its request;
“The expansion requested is to resolve several problems. The first is that when boundaries of the existing places of use were established, small-scale maps were used, and the irrigable areas of the valley floor were not completely covered. As a result, the areas served by the CVP have expanded to that boundary and have, in fact, gone beyond the boundary in a number of places. This presents a dilemma to the United States in that to supply these areas in fulfillment of the commitment to meet inbasin demands, such service may be in technical noncompliance with the project’s water rights. The expansion resolves this problem.
“The second is that certain areas that were authorized to and now receive CVP service were not included in the existing place of use. Notably, certain parts of the San Luis Unit and of the Sacramento Valley Canals Unit as authorized by Congress are not within the existing place of use. The expansion of the place of use will conform it to the CVP service area intended by various [congressional] authorizations. This expansion also anticipates certain future authorizations for areas which can logically and easily be served by the CVP.”
The Bureau proposed a new consolidated and expanded place of use, the boundary of which “generally follows township and range lines, section lines, county lines, or physical boundaries such as stream channels or watersheds.”
In February 1986, the Bureau amended the change petition to include a request to conform the purposes of use in 19 of its CVP permits. The Board described that amendment as follows; “Most of the 19 permits authorize the same major purposes of use. However, different minor purposes of use are
*715
authorized in several of the permits. An amendment to the petition requests that the purposes of use be amended and conformed so that permitted uses of water from all sources are the same.”
In June 1995, the Bureau further amended the change petition to exclude three of the 19 permits. Thus, the Bureau ultimately sought to conform the purposes of use in 16 of its permits. At that time, only two of those 16 permits (permits Nos. 11969 and 11973, both involving the Trinity River) listed “fish & wild life enhancement” or “fish & wildlife propagation” as an authorized purpose of use.
The Bureau explained its request to conform the purposes of use in its permits as follows: “[The Bureau] received assignments of state-filed applications or filed applications for water rights in accordance with acceptable practices at the time the various facilities of the CVP were being planned. It was necessary at the time to request separate permits for different beneficial uses. With the magnitude of the CVP and its integrated operations, however, it was not practical to try to match up a particular beneficial water use to a specific permit. In addition, in 1992, Congress passed the Central Valley Project Improvement Act (CVPIA), which amended the CVP authorizations to include fish and wildlife mitigation, protection and restoration purposes. Consequently, it is important that all of the CVP permits in this petition include the state-defined beneficial use of ‘fish and wildlife preservation and enhancement’ to maximize operational flexibility in order to comply with the CVPIA. [The Bureau] requests that the 16 CVP permits in this petition be amended so that each permit includes the following beneficial uses: irrigation, domestic, municipal, industrial, frost protection, heat control, fish and wildlife preservation and enhancement, salinity control, water quality control, stock-watering and recreation. No changes in operations are contemplated as a result of this request. The Central Valley Project will continue to be operated according to federal legislation including the CVPIA and our water service and settlement contractual arrangements as well as our permit conditions.”
Also in June 1995, the Bureau amended the change petition to request that the place of use in its permits be changed only “to conform to the authorized service areas of districts with existing long-term water service contracts with [the Bureau].” The Bureau characterized this request as one to “conform” or “correct” the existing place of use boundary, rather than as a request to expand that boundary.
In connection with this amendment, the Bureau took “the existing boundary fines on the maps submitted with [the Bureau’s] various CVP [water
*716
right] applications” and “digitized” those lines through the Bureau’s GIS (geographical information system) to create a single line. The Bureau then compared the area inside that line to the authorized district services areas of its contractors and determined that “[t]he present service areas of 26 of [the Bureau’s] contractors have some lands outside of the existing place of use boundary as now defined by [the Bureau’s] GIS system.” One of those districts was Santa Clara Valley Water District (Santa Clara); another was Westlands.
In December 1997, the Board released a draft EIR for the change petition (the change EIR). In analyzing the potential significant environmental effects of approving the Bureau’s request to conform the places of use in its permits to the authorized district service areas, the change EIR distinguished between “encroachment” lands and “expansion” lands. The change EIR defined encroachment lands as “lands that have already received CVP water within the 26 CVP water contractor service areas but are presently outside the authorized [place of use].” Expansion lands were defined as “lands outside the authorized [place of use] that have never received CVP water but are entitled to service under one of the existing 26 CVP water contracts.” The change EIR explained that “[e]ncroached lands are discussed at the project-specific level,” but “[pjotential environmental impacts associated with the expansion areas are discussed on a programmatic level because future land and water uses cannot be readily determined at this time, and would require speculation. Prior to [Board] authorization for delivery of CVP water to expansion lands, more detailed site-specific environmental analysis and site-specific environmental documentation meeting CEQA requirements may be required.” Elsewhere, the change EIR stated: “At present the [Board] and [the Bureau] do not know where water may be used and for what purposes by contractors on the expansion lands. Therefore, no approval to deliver water to expansion lands can be granted until adequate site-specific environmental documentation on expansion land water delivery proposals are completed.”
With respect to the encroachment lands, the change EIR determined that “the development and land use conversion of 49,602 acres was facilitated by delivery of CVP water,” resulting in the alteration of six different kinds of natural habitat. The change EIR concluded that “[t]he impact to these habitats and the associated wildlife species, designated as endangered or threatened in accordance with federal and state endangered species protection mandates, is considered a significant adverse impact” and that “[m]itigation for compensating past impacts to encroachment lands must provide similar environmental/habitat values that were associated with the affected lands.” The change EIR further observed that “[the Bureau] is currently implementing several programs capable of achieving the mitigation requirements described in the PEIR
[sic\.
These programs consist of ongoing, adaptive management efforts that will, overtime [sz'c], restore, create and maintain
*717
targeted environmental habitat values which would mitigate impacts associated with the construction and operation of the CVP. This program is recognized by the [Board] as the appropriate means to obtain mitigation for the impacts to encroachment lands, provided that portions of the funds and management efforts of these ongoing programs would be specifically assigned to mitigating those environmental/habitat values adversely affected by the encroachment of CVP water supplies to the 49,602 acres outside the authorized [place of use].”
The revised notice of public hearing issued by the Board in May 1998 gave notice that phase 7 of the public hearing would address the change petition. “During Phase 7, it became apparent that the maps prepared by the [Bureau] to depict the boundaries of the currently authorized places of use were not consistent with the official place of use maps in the files of the [Board], [f] Consequently, the [Board] received in evidence the official place of use maps and based its technical analysis on a comparison of the official maps with the areas currently being served by the CVP. . . . The analysis shows that seven of the twenty-six CVP contractors whose use of water was addressed in the [draft change EIR] as encroachment outside the place of use are entirely within the current place of use.” (Decision 1641, p. 118.)
Under the Board’s revised analysis, Santa Clara—which has a total service area of 835,200 acres—included 20,912 acres of encroachment lands and 561,199 acres of expansion lands. Westlands—which has a total service area of 605,548 acres—included 30,718 acres of encroachment lands and 9,664 acres of expansion lands.
The Board certified the final change EIR on December 29, 1999.
In Decision 1641, the Board determined the expansion lands could not “be added to the CVP place of use at this time” because the change EIR “analyze[d] the environmental effects of expansion at the programmatic level, which does not provide enough information to approve the expansion areas under CEQA.” The Board noted that these areas “can be added on a case-by-case basis in the future, subject to appropriate CEQA documentation and the approval of the [Board] under Water Code section 1700, et seq., or other provisions of the Water Code.” (Decision 1641, p. 121.)
The Board approved the addition of all the encroachment lands to the authorized place of use in the Bureau’s permits, but imposed habitat mitigation requirements on the Bureau “for all the encroachment land that was first converted to irrigated agriculture due to CVP water deliveries” unless the Bureau could demonstrate the particular encroachment in question was “not subject to CEQA because it occurred before the effective date of CEQA, or
*718
that an exemption from mitigation requirements is justified because the impacts of encroachment have already been mitigated.”
With respect to the Bureau’s request to conform the purposes of use in its permits, the Board approved that request (over Westlands’s objection), which had the effect of adding fish and wildlife enhancement as an authorized purpose of use in 14 of the Bureau’s permits. (Decision 1641, pp. 122-130.)
IV
The Trial Court Proceedings
In January 2000, following the Board’s issuance of its original Decision 1641 but before its issuance of the revised decision, four mandamus petitions were filed challenging the Board’s decision: (1)
Central Delta Water Agency v. State Water Resources Control Board
(Super. Ct. S.F. City and County, 2003, No. 309539); (2)
Anderson
v.
State Water Resources Control Board
(Super. Ct. Fresno County, 2003, No. 645385-6); (3)
San Luis Water District v. State Water Resources Control Board
(Super. Ct. Merced County, 2002, No. 143845); and (4)
Glenn-Colusa Irrigation District v. State Water Resources Control Board
(Super. Ct. Sac. County, 2000, No. 00CS00201). The Board petitioned to have the four cases coordinated. (See Code Civ. Proc., § 404 et seq.) In April 2000, the Chief Justice of California and Chair of the Judicial Council authorized the presiding judge of the Sacramento County Superior Court to assign a coordination motion judge to determine whether coordination of the four actions was appropriate. The Judicial Council gave the coordination proceeding the special title of
SWRCB Cases.
Meanwhile, that same month, following the Board’s issuance of its revised Decision 1641 in March 2000, another seven mandamus petitions were filed challenging the Board’s actions: (1)
Central Delta Water Agency
v.
State Water Resources Control Board
(Super. Ct. S.F. City and County, 2003, No. 311502); (2)
County of San Joaquin
v.
State Water Resources Control Board
(Super. Ct. S.F. City and County, 2003, No. 311499); (3)
Golden Gate Audubon Society
v.
State Water Resources Control Board
(Super. Ct. Alameda County, 2003, No. 825585-9); (4)
Pacific Coast Federation of Fishermen’s Associations v. State Water Resources Control Board
(Super. Ct. S.F. City and County, 2003, No. 311507); (5)
Santa Clara Valley Water District v. State Water Resources Control Board
(Super. Ct. S.F. City and County, 2003, No. 311549); (6)
State Water Contractors v. State Water Resources Control Board
(Super. Ct. Sac. County, 2001, No. 00CS00602); and (7)
Westlands Water District v. State Water Resources Control Board
(Super. Ct. Sac. County, 2003, No. 00CS00603).
*719
In May 2000, the presiding judge of the Sacramento County Superior Court assigned Judge Brian R. Van Camp as the coordination motion judge for the first four cases. In July 2000, Judge Van Camp ordered the cases coordinated, designated this court as the reviewing court with appellate jurisdiction and recommended that the coordinated proceeding be assigned to the Sacramento County Superior Court.
In August, the Chief Justice of California and Chair of the Judicial Council authorized the Presiding Judge of the Sacramento County Superior Court to assign a coordination trial judge. The presiding judge assigned the coordinated proceeding to Judge Roland L. Candee.
In September 2000,
Glenn-Colusa Irrigation District v. State Water Resources Control Board, supra,
No. 00CS00201, was dismissed by stipulation, leaving three cases in the coordinated proceeding.
The next month, the Board filed a petition for coordination of the seven additional cases filed in April 2000 as add-on cases. (See Cal. Rules of Court, rule 1544.) In November 2000, the trial court ordered those seven cases coordinated with the three remaining original cases.
Over the next two and one-half years, two more of the coordinated
cases—State Water Contractors
v.
State Water Resources Control Board, supra,
No. 00CS00602, and
San Luis Water District v. State Water Resources Control Board, supra,
No. 143845—were dismissed, leaving eight cases.
In May 2003, the trial court issued its statement of decision in the coordinated cases. The trial court upheld Decision 1641 with two exceptions.
First, the court concluded that “while the [Vemalis Adaptive Management Plan] and the [San Joaquin River Agreement] are appropriate and permissible steps toward implementation of the 1995 [Bay-Delta] Plan, they do not satisfy at all times of the year the flow requirements of the 1995 Plan. These are the legal minimum flow objectives that must be satisfied unless changed in an appropriate proceeding to modify the 1995 Plan itself.” Accordingly, the court granted relief on the twelfth cause of action in the mandamus petition in
Central Delta Water Agency
v.
State Water Resources Control Board, supra,
No. 311502, and ordered that a writ issue directing the Board to conduct
*720
further proceedings to fully assign responsibility for meeting all of the flow objectives in the 1995 Bay-Delta Plan or modify the objectives in the plan.
18
Second, the trial court concluded that when the Legislature merged Westlands with another water district in 1965, “the [L]egislature effectuated a statutory authorization for the delivery of federal CVP water to all of the lands of the combined . . . district.” Accordingly, the trial court granted the mandamus petition in
Anderson v. State Water Resources Control Board, supra,
No. 645385-6, and ordered the issuance of a writ directing the Board to conform the places of use under the Bureau’s CVP permits to include both the encroachment and expansion lands within Westlands without any mitigation requirement.
Judgments in seven of the coordinated cases were entered on June 19, 2003. The judgment in the eighth case (Anderson) was entered on July 16, 2003.
Eight timely notices of appeal and three timely notices of cross-appeal were filed in seven of the cases. No appeal was taken in
Pacific Coast Federation of Fishermen’s Associations
v.
State Water Resources Control Board, supra,
No. 311507.
DISCUSSION
I
Standard of Review
We begin our discussion by setting out the standards of review that apply to the appeals in these coordinated cases.
A
Water Rights Decisions
“In undertaking to allocate water rights, the Board performs an adjudicatory function.”
(United States v. State Water Resources Control Bd.,
*721
supra,
182 Cal.App.3d at p. 113 .) Accordingly, Code of Civil Procedure section 1094.5 applies to a writ proceeding seeking to challenge a water rights decision by the Board. (§ 1126.) “The inquiry in such a case shall extend to the questions whether the [Board] has proceeded without, or in excess of jurisdiction; whether there was a fair trial; and whether there was any prejudicial abuse of discretion. Abuse of discretion is established if the [Board] has not proceeded in the manner required by law, the order or decision is not supported by the findings, or the findings are not supported by the evidence.” (Code Civ. Proc., § 1094.5, subd. (b).) “Where it is claimed that the findings are not supported by the evidence, in cases in which the court is authorized by law to exercise its independent judgment on the evidence, abuse of discretion is established if the court determines that the findings are not supported by the weight of the evidence. In all other cases, abuse of discretion is established if the court determines that the findings are not supported by substantial evidence in the light of the whole record.”
(Id.,
subd. (c).)
The trial court is authorized by law to exercise its independent judgment on the evidence when “the right or interest affected by the administrative decision is a ‘vested’ one.”
(Merrill v. Department of Motor Vehicles
(1969) 71 Cal.2d 907, 914 [ 80 Cal.Rptr. 89 , 458 P.2d 33 ], fin. omitted.) “If the right affected is ‘vested’ the decision is reviewed by means of a limited trial de novo in which the trial court not only examines the record for errors of law but also exercises its independent judgment upon the weight of the evidence produced before the administrative agency together with any further evidence properly admitted by the court. [Citations.] If, on the other hand, the right is not ‘vested’ the trial court’s scope of review extends only to matters of law appearing on the record of the administrative proceeding, and accordingly its review of the evidence produced below is limited to a determination of whether it is legally sufficient to sustain the decision.”
(Id.
at pp. 914—915, fns. and italics omitted.)
“In a case wherein the trial court is authorized to conduct a limited trial de novo ... the province of the appellate court is analogous to that assumed by it in an ordinary civil appeal: only errors of law are subject to its cognizance, and a factual finding can be overturned only if the evidence received by the trial court, including the record of the administrative proceeding, is insufficient as a matter of law to sustain the finding. [Citations.] In a case wherein no limited trial de novo is authorized by law, however, the trial court itself exercises an essentially appellate function in that only errors of law appearing on the administrative record are subject to its cognizance. In such a case, therefore, the trial and appellate courts occupy identical positions with regard
*722
to the administrative record, and the function of the appellate court, like that of the trial court, is to determine whether that record is free from legal error.”
(Merrill v. Department of Motor Vehicles, supra,
71 Cal.2d at pp. 915-916.)
Of course, questions of law are subject to de novo review. (E.g.,
Pollak v. State Personnel Bd.
(2001) 88 Cal.App.4th 1394, 1404 [ 107 Cal.Rptr.2d 39 ].) The proper interpretation of a statute, and its application to undisputed facts, is a question of law.
(Smith
v.
Rae-Venter Law Group
(2002) 29 Cal.4th 345, 357 [ 127 Cal.Rptr.2d 516 , 58 P.3d 367 ].)
The Board argues that the interpretations it has given to various Water Code provisions in Decision 1641 and its order on reconsideration are entitled to deference and “should not be overturned, unless clearly erroneous.” We disagree. As our Supreme Court recently explained:
“An agency interpretation of the meaning and legal effect of a statute is entitled to consideration and respect by the courts; however, unlike quasi-legislative regulations adopted by an agency to which the Legislature has confided the power to ‘make law,’ and which, if authorized by the enabling legislation, bind this and other courts as firmly as statutes themselves, the binding power of an agency’s
interpretation
of a statute or regulation is contextual: Its power to persuade is both circumstantial and dependent on the presence or absence of factors that support the merit of the interpretation. Justice Mosk may have provided the best description when he wrote . . . that ‘ “The appropriate degree of judicial scrutiny in any particular case is perhaps not susceptible of precise formulation, but lies somewhere along a continuum with nonreviewability at one end and independent judgment at the other.” [Citation.] Quasi-legislative administrative decisions are properly placed at that point of the continuum at which judicial review is more deferential; ministerial and informal actions do not merit such deference, and therefore lie toward the opposite end of the continuum.’ [Citations.]
“Courts must, in short, independently judge the text of the statute, taking into account and respecting the agency’s interpretation of its meaning, of course, whether embodied in a formal rule or less formal representation. Where the meaning and legal effect of a statute is the issue, an agency’s interpretation is one among several tools available to the court. Depending on the context, it may be helpful, enlightening, even convincing. It may sometimes be of little worth. [Citation.] Considered alone and apart from the context and circumstances that produce them, agency interpretations are not binding or necessarily even authoritative. To quote the statement of the Law Revision Commission in a recent report, ‘The standard for judicial review of
*723
agency interpretation of law is the
independent judgment
of the court, giving
deference
to the determination of the agency
appropriate
to the circumstances of the agency action.’ ”
(Yamaha Corp. of America v. State Bd. of Equalization
(1998) 19 Cal.4th 1, 7-8 [ 78 Cal.Rptr.2d 1 , 960 P.2d 1031 ].)
Based on the foregoing, in interpreting the various Water Code provisions at issue in this case, we will exercise our independent judgment, giving deference to the Board’s interpretation only if the Board shows that such deference is warranted by the circumstances.
B
CEQA Actions
In a mandate proceeding to review an agency’s decision for compliance with CEQA, we review the administrative record to determine whether the agency abused its discretion.
(Save Our Peninsula Committee
v.
Monterey County Bd. of Supervisors
(2001) 87 Cal.App.4th 99, 116-117 [ 104 Cal.Rptr.2d 326 ].) “Abuse of discretion is shown if (1) the agency has not proceeded in a manner required by law, or (2) the determination is not supported by substantial evidence.”
(Gentry v. City of Murrieta
(1995) 36 Cal.App.4th 1359, 1375 [ 43 Cal.Rptr.2d 170 ].) “When the informational requirements of CEQA are not complied with, an agency has failed to proceed in ‘a manner required by law’ and has therefore abused its discretion.”
(Save Our Peninsula Committee,
at p. 118.) Furthermore, “when an agency fails to proceed as required by CEQA, harmless error analysis is inapplicable. The failure to comply with the law subverts the purposes of CEQA if it omits material necessary to informed decisionmaking and informed public participation. Case law is clear that, in such cases, the error is prejudicial.”
(County of Amador v. El Dorado County Water Agency
(1999) 76 Cal.App.4th 931, 946 [ 91 Cal.Rptr.2d 66 ].)
“In reviewing an agency’s decision to certify an EIR, we presume the correctness of the decision. The project opponents thus bear the burden of proving that the EIR is legally inadequate.”
(Save Our Peninsula Committee v. Monterey County Bd. of Supervisors, supra,
87 Cal.App.4th at p. 117 .) However, “[w]hile we may not substitute our judgment for that of the decision makers, we must ensure strict compliance with the procedures and mandates of the statute.”
(Id.
at p. 118.)
*724
II
Challenges to Implementation of the 1995 Water Quality Control Plan for the Bay-Delta
A
The Central Delta Parties’ Challenges to Implementation of the 1995 Bay-Delta Plan
In April 2000, six parties with interests in the central Delta
19
filed a petition for writ of mandate seeking to vacate Decision 1641 on non-CEQA grounds.
20
(Central Delta Water Agency
v.
State Water Resources Control Board, supra,
No. 311502.) This
Central Delta
case was one of the cases added to the coordinated proceeding in November 2000.
The Central Delta parties’ non-CEQA writ petition raised many issues, most of which we address directly below. Some of the issues we will address later, in conjunction with related issues raised by other parties.
1.
Challenges to the San Joaquin River Agreement
a.
Implementing the Vernalis Pulse Flow Objective and the Southern Delta Salinity Objectives
In the twelfth cause of action in their non-CEQA writ petition, the Central Delta parties alleged, among other things, that in adopting Decision 1641, the Board “failed to implement the 1995 Water Quality Control Plan,” including the “Vernalis Salinity objectives” and the “Vernalis Fish Flow objectives.” They further alleged that the Board “wrongfully modified” the 1995 Bay-Delta Plan “through inadequate implementation.”
Although acknowledging that “[m]any factors weigh in support of’ the San Joaquin River Agreement and the Vernalis Adaptive Management Plan, the trial court concluded the Vernalis flow objectives were “the legal minimum flow objectives that must be satisfied unless changed in an appropriate proceeding to modify the 1995 Plan itself.” The court explained that “[t]o sanction the Board’s action here would effectively allow the Board to change
*725
the no longer challengeable 1995 Plan’s objectives unilaterally without completing the necessary legal steps allowing for interested parties’ input, comments, and challenges.” Accordingly, the court entered a judgment granting the Central Delta parties’ mandamus petition “on the ground that the approval of the San Joaquin River Agreement and the Vemalis Adaptive Management Plan flows for the April-May pulse flow period do not fully satisfy the flow-dependent objectives of the 1995” Bay-Delta Plan. The judgment ordered the issuance of a writ of mandate “commanding the . . . Board to commence further proceedings consistent with the STATEMENT OF DECISION. As to all other causes of action, the petition for writ of mandate is DENIED.” In its statement of decision, the court explained that the writ of mandate would “remand[] this portion of D-1641 to the [Board] for further proceedings [to either] fully assign responsibility for meeting all of the flow-dependent objectives or modify the 1995 Plan objectives.”
The trial court did not address the issue of whether Decision 1641 adequately implemented the southern Delta salinity objectives.
Some of the parties to the San Joaquin River Agreement—namely, San Joaquin River Group Authority and its member agencies, San Joaquin River Exchange Contractors Water Authority and its member agencies, Friant Water Users Authority, and the City and County of San Francisco (collectively San Joaquin River Group)—filed a timely notice of appeal from the part of the judgment that granted the Central Delta parties’ writ petition. After the Central Delta parties filed a timely notice of appeal from the remainder of the judgment (i.e., from the denial of their mandamus petition on all other grounds), three other parties to the San Joaquin River Agreement—State Water Contractors, Kern County Water Agency, and Metropolitan Water District of Southern California (collectively State Water Contractors)—filed a timely notice of cross-appeal from the part of the judgment that granted the mandamus petition. The Board also filed a timely notice of cross-appeal from that part of the judgment. Thus, one appeal and two cross-appeals challenge the trial court’s ruling that the Board’s approval of the San Joaquin River Agreement does not fully satisfy the flow-dependent objectives of the 1995 Bay-Delta Plan.
For their part, in their appeal the Central Delta parties argue, among other issues, that the Board failed to implement the southern Delta salinity objectives from the 1995 Bay-Delta Plan.
i.
The Vemalis Pulse Flow Objective
We first address the trial court’s ruling that the Board failed to implement the Vemalis pulse flow objective. In their challenges to that mling, San
*726
Joaquin River Group, State Water Contractors, and the Board each argue that the 1995 Bay-Delta Plan allowed for staged implementation of the Vemalis pulse flow objective, and the Board’s decision to adopt the San Joaquin River Agreement and its alternate flows during an interim, experimental stage was both authorized and reasonable. We disagree.
Because a water quality control plan is quasi-legislative
(State Water Resources Control Bd. v. Office of Admin. Law, supra,
12 Cal.App.4th at pp. 701-702), we construe the requirements of the 1995 Bay-Delta Plan independently of the trial court, with appropriate deference to the Board’s interpretation. “ ‘The interpretation of a regulation, like the interpretation of a statute, is, of course, a question of law, and while an administrative agency’s interpretation of its own regulation obviously deserves great weight, the ultimate resolution of such legal questions rests with the courts.’ (Citations omitted.) [Citation.] However, the court generally will not depart from the agency’s interpretation unless it is clearly erroneous or unauthorized.”
(Physicians & Surgeons Laboratories, Inc. v. Department of Health Services
(1992) 6 Cal.App.4th 968, 986-987 [ 8 Cal.Rptr.2d 565 ].)
We begin by addressing the Board’s characterization of its action as a “staged implementation” of the Vemalis pulse flow objective. We believe that characterization is inaccurate. In our view, the Board’s action was a
delayed
implementation of the objective, accompanied by the immediate implementation of an alternate (albeit temporary) experimental flow regime which, by the Board’s own admission, provided for the possibility of a lesser flow than the Vemalis pulse flow objective.
Nevertheless, regardless of whether the Board’s implementation of the Vemalis pulse flow objective was “staged” or “delayed,” the real question is whether anything in the 1995 Bay-Delta Plan authorized the Board to implement a temporary, experimental flow regime that might not provide as much water as the Vemalis pulse flow objective. We find no such provision.
As we have previously explained, a water quality control plan must include water quality objectives and a program of implementation needed for achieving those objectives. (§ 13050, subd. (j).) Moreover, the program of implementation must include “[a] description of the nature of actions which are necessary to achieve the objectives” and “[a] time schedule for the actions to be taken.” (§ 13242, subds. (a), (b).)
In Decision 1641, the Board relied on the “time schedule” provision of section 13242 to justify its approval of the San Joaquin River Agreement flow regime as an “interim” requirement. On appeal, the Board likewise argues that “[t]he [Vemalis Adaptive Management Plan] experimental period constitutes a
*727
‘time schedule’ for meeting the [flow] objectives” in the 1995 Bay-Delta Plan. The first flaw in that argument is that, by law, the time schedule for the actions to be taken to achieve objectives in a water quality control plan must be included
as part of the plan itself
(§ 13242.) The 1995 Bay-Delta Plan contains nothing about “[t]he [Vemalis Adaptive Management Plan] experimental period.” The Board must point to a time schedule
in the 1995 Bay-Delta Plan
that authorized it to postpone implementing the Vemalis pulse flow objective. The Board has failed to identify any such provision.
The second flaw in the Board’s argument is that, regardless of the timing issue, the Board has failed to identify anything in the plan that authorized it to implement a flow objective
other
than the Vemalis pulse flow objective, even temporarily. The Vemalis pulse flow objective required a minimum monthly average flow of water at a particular point in the San Joaquin River for a 31-day period in April and May each year, ranging from 3,110 to 8,620 cubic feet per second. Nothing in the 1995 Bay-Delta Plan authorized the Board to implement a different flow regime that could provide less than that amount of water.
This same flaw defeats arguments made by San Joaquin River Group and State Water Contractors. San Joaquin River Group contends that under the 1995 Bay-Delta Plan, because there was no specific schedule for achieving the Vemalis pulse flow objective, the Plan provided that implementation
“should
be immediate.” San Joaquin River Group then argues at length about the meaning of the word “should,” concluding that because “should” is generally permissive and advisory, the Board had the power
not
to implement the Vemalis pulse flow objective immediately and instead provide for a staged implementation. San Joaquin River Group points to nothing in the plan, however, that authorized the Board to implement a
different
flow objective than the Vemalis pulse flow objective, even on a temporary basis.
For its part, State Water Contractors point to the provision in the 1995 Bay-Delta Plan where the Board recommended that the Department and the Bureau “should conduct experiments to investigate and evaluate the biological benefits of pulse flows to move planktonic fish eggs and larvae into Suisun Bay.” (1995 Bay-Delta Plan, p. 38.) According to State Water Contractors, this provision supports a reading of the 1995 Bay-Delta Plan allowing for staged implementation of the Vemalis pulse flow requirement, because “when the Board . . . embraced the Vemalis Adaptive Management Plan ... it did exactly what it said it would do in the implementation program of the” 1995 Bay-Delta Plan. Like the Board and San Joaquin River Group, however, State Water Contractors fail to point to anything in the plan that authorized the Board to implement a flow objective different than the Vemalis pulse flow objective. Contrary to State Water Contractors’ suggestion, it is far from apparent that the experiments the Board recommended
*728
could not be conducted under the flow objectives provided for in the 1995 Bay-Delta Plan. In any event, even if those experiments did require flows that were less than those required by the 1995 Bay-Delta Plan, the 1995 Bay-Delta Plan cannot reasonably be read as authorizing the Board to implement a lesser flow regime during the water rights proceeding that was to follow the plan’s adoption.
It is critical to note that the recommended experiments to which State Water Contractors refer were not part of the component of the program of implementation designed to achieve the flow objectives of the 1995 Bay-Delta Plan. Instead, they were part of a different component— recommendations to improve habitat conditions. In introducing those recommendations, the Board explained that “[t]here are numerous actions that can be taken,
in addition to establishing and implementing water quality objectives for the Bay-Delta Estuary,
to improve fish and wildlife beneficial uses in the Estuary.” (1995 Bay-Delta Plan, p. 33, italics added.) One such action was the recommended experiments. Thus, the experiments were expressly intended as actions
additional
to those needed to achieve the flow objectives of the 1995 Bay-Delta Plan. The Board’s recommendation of these experiments in the plan cannot reasonably be read as allowing the Board to implement in Decision 1641 an experimental flow regime in lieu of the plan’s Vemalis pulse flow objective, even temporarily.
We agree with State Water Contractors, in the abstract, that the “careful, sequential implementation of a water quality objective important to fish and other competing beneficial uses of water is compatible with the requirements of the Porter-Cologne Act.” We cannot agree, however, that the 1995 Bay-Delta Plan actually
provided
for a sequential implementation of the Vemalis pulse flow objective, with the first stage to consist of an experimental flow regime that could provide smaller flows. In the plan of implementation in the 1995 Bay-Delta Plan, the Board specified that it would “address the water supply-related objectives in this plan”—including the objectives for “river flow”—in a later “water rights proceeding . . . through the amendment of water rights under the authority of the [Board].” The Board further stated that “[t]he water right decision . . .
will
allocate responsibility for meeting the objectives among water rights holders in the Bay-Delta Estuary watershed.” (1995 Bay-Delta Plan, p. 27, italics added.) No provision was made for allocating responsibility to meet any objectives other than those specified in the 1995 Bay-Delta Plan.
Of course, had the proposal for the San Joaquin River Agreement and the Vemalis Adaptive Management Plan been made during the hearings on the 1995 Bay-Delta Plan, the Board might have adopted the temporary experimental flow regime as a part of the river flow objectives in the 1995
*729
Bay-Delta Plan, based on a determination that the experimental flows would help “ensure the reasonable protection of beneficial uses” by helping the Board determine what flows are most optimal to enhance the survival of fish in the San Joaquin River. (§ 13241.) Or, perhaps, when the proposal for the San Joaquin River Agreement and the Vemalis Adaptive Management Plan was presented to the Board in the water rights proceeding, the Board could have sought to conduct a regulatory proceeding to amend the 1995 Bay-Delta Plan before completing the water rights proceeding. But the Board could not properly adopt the San Joaquin River Agreement’s alternate flow regime, even on a temporary basis, in the water rights proceeding under the guise of a “staged implementation” of the objectives in the 1995 Bay-Delta Plan, because that “staged implementation” fundamentally altered those objectives, and such an alteration could be accomplished only through a properly noticed and conducted regulatory proceeding.
21
(See § 13244.)
Contrary to State Water Contractors’ assertion, the trial court’s decision does not rest on “the assumption that water right decisions adopted by the . . . Board must provide for full and immediate implementation of the water quality objectives set forth in any applicable water quality control plan.” The trial court’s decision rests on the conclusion (with which we agree) that when a water quality control plan calls for a particular flow objective to be achieved by allocating responsibility to meet that objective in a water rights proceeding, and the plan does
not
provide for any alternate, experimental flow objective to be met on an interim basis, the decision in that water rights proceeding must fully implement the flow objective provided for in the plan. The guiding principle is that the Board’s power to act in a water rights proceeding commenced to implement a water quality control plan is constrained by the terms of the plan it is implementing.
The Board disagrees, contending that “[njothing in the Porter-Cologne Act mandates the . . . Board to adopt all of the flow-dependent objectives in a water quality control plan when it issues a water right decision.” According to the Board, it is required only to “consider” such objectives; it is not required to implement them.
*730
Section 13247—part of the Porter-Cologne Act—provides that “[s]tate offices, departments, and boards, in carrying out activities which may affect water quality,
shall
comply with water quality control plans approved or adopted by the state board unless otherwise directed or authorized by statute .. . .” (Italics added.) Here, in the plan of implementation in the 1995 Bay-Delta Plan, the Board specifically stated that “[t]he water right decision . . .
will
allocate responsibility for meeting the [water supply-related] objectives among water rights holders in the Bay-Delta Estuary watershed . . . .” (1995 Bay-Delta Plan, p. 27, italics added.) Thus, the 1995 Bay-Delta Plan specifically identified this water rights proceeding and Decision 1641 as the action “necessary to achieve the [river flow] objectives” of the 1995 Bay-Delta Plan, including the Vemalis pulse flow objective. (§ 13242, subd. (a).) Certainly, in conducting a water rights proceeding for the express purpose of allocating responsibility for meeting a water quality objective in a water quality control plan, the Board is “carrying out [an] activit[y] which may affect water quality.” (§ 13247.) Accordingly, the Board was compelled by section 13247 to comply with the 1995 Bay-Delta Plan unless another statute authorized the Board
not
to comply with the plan.
The Board first challenges the premise that it committed itself in the 1995 Bay-Delta Plan to implementing the flow objectives of the plan. The Board points to language in the last paragraph of the part of the program of implementation that addressed river flows, which stated, “These flows will be considered by the [Board] in its allocation of responsibility among the water rights holders in the watershed during the water rights proceeding.” (1995 Bay-Delta Plan, p. 28.) According to the Board, this language “acknowledges that the . . . Board’s implementation responsibility as to the San Joaquin River flows is to ‘consider’ such objectives in the follow-on water right proceedings.”
This argument fails because the Board takes the language on which it relies out of context. The paragraph on which the Board relies expressly addresses the “interim flows” that the Bureau was to provide “[pjrior to adoption of the water rights decision.” Thus, the Board was merely stating that it would consider those interim flows when it allocated responsibility for the plan’s flow objectives in the water rights proceeding. The Board was
not
stepping back from its commitment to actually allocate responsibility for the flow objectives in that proceeding.
The Board also refers to portions of the EIR that it prepared in connection with the 1995 Bay-Delta Plan and contends that those passages show “the . . . Board expressly envisioned that [it] might reevaluate the San Joaquin River pulse flow requirements in the follow-on water right decision.” This argument is meaningless. Whether the Board envisioned a reevaluation of the Vemalis
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pulse flow objective during the water rights proceeding, we have decided already that the Board had no power to
change
that objective in that proceeding. The question that remains is whether the Board had the statutory authority not to comply with its own water quality control plan, in which it committed itself to implement a flow objective by allocating the responsibility for meeting that objective among the appropriate water right holders in a water rights proceeding. The Board has failed to identify any such authority.
To provide such authority, the Board relies on sections 1257 and 1258, which specify what factors the Board must consider “[i]n acting upon application to appropriate water.” (§ 1257.) Section 1257 requires the Board to “consider the relative benefit to be derived from (1) all beneficial uses of the water concerned including, but not limited to . . . any uses specified to be protected in any relevant water quality control plan . . . .” More directly, section 1258 provides that the Board “shall consider water quality control plans which have been established pursuant to Division 7 (commencing with Section 13000) of this code, and
may
subject such appropriations to such terms and conditions as it finds are necessary to carry out such plans.” (Italics added.) According to the Board, these provisions “expressly grant the . . . Board the discretionary authority to apply the quasi-legislative requirements of the water quality control plans when adopting quasi-judicial water right decisions such as D-1641.”
Even assuming for the sake of argument that in conducting the water rights proceeding at issue here the Board was “acting upon application to appropriate water,”
22
we conclude the Board’s reliance on sections 1257 and 1258 is misplaced. In effect, the Board’s position is that the word “may” in section 1258 gives it the discretion to decide whether “to implement all aspects of a water quality control plan,” even if (as here) the plan itself evidences a commitment by the Board to do so. This position is based on the unspoken premise that “may,” in this context, denotes the right, but not the obligation, to act.
This premise is contrary to well-established precedent. As our Supreme Court explained in
Mass v. Board of Education
(1964) 61 Cal.2d 612 [ 39 Cal.Rptr. 739 , 394 P.2d 579 ], in response to another public entity’s attempt to avoid a statutory obligation, “Although the word ‘may’ customarily implies permissiveness [citation], words must be construed in their textual context. [Citation.] The word ‘may’ here occurs in a statute defining a public duty. ‘ “Words permissive in form, when a public duty is involved, are considered mandatory.” ’ ”
(Id.
at pp. 616, 622-623, quoting
Harless
v.
Carter
(1954) 42 Cal.2d 352, 356 [ 267 P.2d 4 ].) “ ‘[W]here the purpose of the law is to cloth
*732
public officers with power to be exercised for the benefit of third persons, or for the public at large—that is, where the public interest or private right requires that a thing should be done—then the language, though permissive in form, is peremptory.’ ”
(Harless v. Carter, supra,
42 Cal.2d at p. 357 , quoting
County of Los Angeles v. State
(1923) 64 Cal.App. 290, 295 [ 222 P. 153 ].)
Here, the power to be exercised—the power to subject appropriative water rights to terms and conditions necessary to carry out water quality control plans—is undoubtedly a power to be exercised for the public at large. Thus, the word “may” in section 1258 is mandatory, not permissive, and that statute did not exempt the Board from the obligation imposed by section 13247 to comply with its own water quality control plan.
It has been noted that “the principal enforcement mechanism available to the Board [to enforce compliance with water quality control plans] is its regulation of water rights . . . .”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 125 , italics omitted.) It would be strange if the Board, having determined in a water quality control plan that a water rights proceeding was necessary to achieve the water quality objectives in that plan, could simply decide
not
to take action in that proceeding and thereby refuse to enforce its own plan. Fortunately, the Legislature has not authorized the Board to do any such thing. Thus, the Board cannot—as it attempted to do here—make a de facto amendment to a water quality objective in a water quality control plan by simply refusing to take the action that it has identified as necessary to achieve that objective.
The Board contends the decision in
United States v. State Water Resources Control Bd., supra,
182 Cal.App.3d at pages 143-144, “has affirmed the . . . Board’s water right discretion regarding plan objectives.” In the combined regulatory/adjudicatory proceeding underlying that decision, the Board generally employed “a so-called ‘without project’ level of protection” in adopting revised water quality objectives for the Delta.
(Id.
at p. 115.) The Board did not employ that level of protection in all of its water quality objectives, however. For example, “the Board determined that to maintain ‘without project’ standards of water quality at Antioch to protect the rights of the Antioch riparians [who used the water for an industrial use that was sensitive to salt] would require a wasteful release of 25 acre-feet of outflow for each acre-foot diverted.”
(Id.
at p. 143.) Rather than require such an unreasonable waste of water, “the Board eliminated the Antioch standard from the Plan,” “accepted the offer of [the Department] to provide a substitute supply to the Antioch riparians through the Contra Costa Canal,” “and required the projects only to meet the standards for the canal.”
(Id.
at pp. 143-144.) On appeal, the court concluded, “the Board had little choice but to exempt the projects from the Antioch standards” “[i]n light of the
*733
constitutional mandate proscribing unreasonable or wasteful use of water (Cal. Const., art. X, § 2).”
(United States
v.
State Water Resources Control Bd., supra,
182 Cal.App.3d at p. 144 .)
The Board interprets this part of the court’s decision as “affirming] the . . . Board’s deviation from the ‘without project’ standard” based on “the [constitutional] prohibition against waste and unreasonable use.” Thus, according to the Board, the decision in
United States v. State Water Resources Control Bd.
affirms the Board’s power to disregard objectives in a water quality control plan.
The Board has misread the case on which it relies. The fact that the proceeding underlying that case encompassed both the regulatory proceeding to amend the water quality control plan for the Delta, and the adjudicatory proceeding to implement that plan by modifying existing water rights, may have led to the Board’s confusion. Although the court did, at one point, characterize the B

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Source: Frix Law Library, https://www.frixlaw.com/law-library/cases/2244615. Public record. Not legal advice.