# Endangered and Threatened Wildlife and Plants; 12-Month Finding on a Petition to List the San Francisco Bay-Delta Population of the Longfin Smelt as Endangered or Threatened

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URL: https://www.frixlaw.com/law-library/documents/fr%3A2012-7198

## Record

- **Collection:** Federal Register
- **Document type:** Proposed Rule
- **Published:** April 2, 2012
- **Citation:** 77 FR 19756

## Text

DEPARTMENT OF THE INTERIOR
Fish and Wildlife Service
50 CFR Part 17
[Docket No. FWS-R8-ES-2008-0045: 4500030113]
Endangered and Threatened Wildlife and Plants; 12-Month Finding on a Petition to List the San Francisco Bay-Delta Population of the Longfin Smelt as Endangered or Threatened

AGENCY:

Fish and Wildlife Service, Interior.

ACTION:

Notice of 12-month petition finding.

SUMMARY:

We, the U.S. Fish and Wildlife Service (Service), announce a 12-month finding on a petition to list the San Francisco Bay-Delta distinct population segment (Bay Delta DPS) of longfin smelt as endangered or threatened and to designate critical habitat under the Endangered Species Act of 1973, as amended (Act). After review of the best available scientific and commercial information, we find that listing the longfin smelt rangewide is not warranted at this time, but that listing the Bay-Delta DPS of longfin smelt is warranted. Currently, however, listing the Bay-Delta DPS of longfin smelt is precluded by higher priority actions to amend the Lists of Endangered and Threatened Wildlife and Plants. Upon publication of this 12-month finding, we will add the Bay-Delta DPS of longfin smelt to our candidate species list. We will develop a proposed rule to list the Bay-Delta DPS of longfin smelt as our priorities allow. We will make any determinations on critical habitat during the development of the proposed listing rule. During any interim period, we will address the status of the candidate taxon through our annual Candidate Notice of Review (CNOR).

DATES:

The finding announced in this document was made on April 2, 2012.

ADDRESSES:

This finding is available on the Internet at
http://www.regulations.gov
at Docket Number [FWS-R8-ES-2008-0045]. Supporting documentation we used in preparing this finding is available for public inspection, by appointment, during normal business hours at the U.S. Fish and Wildlife Service, San Francisco Bay-Delta Fish and Wildlife Office, 650 Capitol Mall, Sacramento, CA 95814. Please submit any new information, materials, comments, or questions concerning this finding to the above street address.

FOR FURTHER INFORMATION CONTACT:

Mike Chotkowski, Field Supervisor, San Francisco Bay-Delta Fish and Wildlife Office (see
ADDRESSES
); by telephone at 916-930-5603; or by facsimile at 916-930-5654
mailto:.
If you use a telecommunications device for the deaf (TDD), please call the Federal Information Relay Service (FIRS) at 800-877-8339.

SUPPLEMENTARY INFORMATION:

Background

Section 4(b)(3)(B) of the Endangered Species Act of 1973, as amended (Act) (16 U.S.C. 1531
et seq.
), requires that, for any petition to revise the Federal Lists of Endangered and Threatened Wildlife and Plants that contains substantial scientific or commercial information that listing the species may be warranted, we make a finding within 12 months of the date of receipt of the petition. In this finding, we will determine that the petitioned action is: (1) Not warranted, (2) warranted, or (3) warranted, but the immediate proposal of a regulation implementing the petitioned action is precluded by other pending proposals to determine whether species are endangered or threatened, and expeditious progress is being made to add or remove qualified species from the Federal Lists of Endangered and Threatened Wildlife and Plants. Section 4(b)(3)(C) of the Act requires that we treat a petition for which the requested action is found to be warranted but precluded as though resubmitted on the date of such finding, that is, requiring a subsequent finding to be made within 12 months. We must publish these 12-month findings in the
Federal Register
.

Previous Federal Actions

On November 5, 1992, we received a petition from Mr. Gregory A. Thomas of the Natural Heritage Institute and eight co-petitioners to add the longfin smelt (
Spirinchus thaleichthys
) to the List of Endangered and Threatened Wildlife and designate critical habitat in the Sacramento and San Joaquin Rivers and estuary. On July 6, 1993, we published a 90-day finding (58 FR 36184) in the
Federal Register
that the petition contained substantial information indicating the requested action may be warranted, and that we would proceed with a status review of the longfin smelt. On January 6, 1994, we published a notice of a 12-month finding (59 FR 869) on the petition to list the longfin smelt. We determined that the petitioned action was not warranted, based on the lack of population trend data for estuaries in Oregon and Washington, although the southernmost populations were found to be declining. Furthermore, we found the Sacramento-San Joaquin River estuary population of longfin smelt was not a distinct population segment (DPS) because we determined that the population was not biologically significant to the species as a whole, and did not appear to be sufficiently reproductively isolated.

On August 8, 2007, we received a petition from the Bay Institute, the Center for Biological Diversity, and the Natural Resources Defense Council to list the San Francisco Bay-Delta (hereafter referred to as the Bay-Delta) population of the longfin smelt as a DPS and designate critical habitat for the DPS concurrent with the listing. On May 6, 2008, we published a 90-day finding (73 FR 24911) in which we concluded that the petition provided substantial information indicating that listing the Bay-Delta population of the longfin smelt as a DPS may be warranted, and we initiated a status review. On April 9, 2009, we published a notice of a 12-month finding (74 FR 16169) on the August 8, 2007, petition. We determined that the Bay-Delta population of the longfin smelt did not meet the discreteness element of our DPS policy and, therefore, was not a valid DPS. We therefore determined that the Bay-Delta population of the longfin smelt was not a listable entity under the Act.

On November 13, 2009, the Center for Biological Diversity filed a complaint in U.S. District Court for the Northern District of California, challenging the Service on the merits of the 2009 determination. On February 2, 2011, the Service entered into a settlement agreement with the Center for Biological Diversity and agreed to conduct a rangewide status review and prepare a 12-month finding to be published by September 30, 2011. In the event that the Service determined in the course of the status review that the longfin smelt does not warrant listing as endangered or threatened over its entire range, the Service agreed to consider whether any population of longfin smelt qualifies as a DPS. In considering whether any population of longfin smelt qualifies as a DPS, the Service agreed to reconsider whether the Bay-Delta population of the longfin smelt constitutes a DPS. At the request of the Service, Department of Justice requested an extension from the Court to allow for a more comprehensive review of new information pertaining to the longfin smelt and to seek the assistance of two expert panels to assist us with that review. The plaintiffs filed a motion of non-opposition, and on October 3, 2011, the court granted an extension to March

23, 2012 for the publication of a new 12-month finding.

Species Information

Species Description and Taxonomy

Longfin smelt measure 9-11 centimeters (cm) (3.5-4.3 inches (in)) standard length, although third-year females may grow up to 15 cm (5.9 in). The sides and lining of the gut cavity appear translucent silver, the back has an olive to iridescent pinkish hue, and mature males are usually darker in color than females. Longfin smelt can be distinguished from other smelts by their long pectoral fins, weak or absent striations on their opercular (covering the gills) bones, incomplete lateral line, low numbers of scales in the lateral series (54 to 65), long maxillary bones (in adults, these bones extend past mid-eye, just short of the posterior margin of the eye), and lower jaw extending anterior of the upper jaw (Mcallister 1963, p. 10; Miller and Lea 1972, pp. 158-160; Moyle 2002, pp. 234-236).

The longfin smelt belongs to the true smelt family Osmeridae and is one of three species in the
Spirinchus
genus; the night smelt (
Spirinchus starksi
) also occurs in California, and the shishamo (
Spirinchus lanceolatus
) occurs in northern Japan (McAllister 1963, pp. 10, 15). Because of its distinctive physical characteristics, the Bay-Delta population of longfin smelt was once described as a species separate from more northern populations (Moyle 2002, p. 235). McAllister (1963, p. 12) merged the two species
S. thaleichthys
and
S. dilatus
because the difference in morphological characters represented a gradual change along the north-south distribution rather than a discrete set. Stanley
et al.
(1995, p. 395) found that individuals from the Bay-Delta population and Lake Washington population differed significantly in allele (proteins used as genetic markers) frequencies at several loci (gene locations), although the authors also stated that the overall genetic dissimilarity was within the range of other conspecific fish species. They concluded that longfin smelt from Lake Washington and the Bay-Delta are conspecific (of the same species) despite the large geographic separation.

Delta smelt and longfin smelt hybrids have been observed in the Bay-Delta estuary, although these offspring are not thought to be fertile because delta smelt and longfin smelt are not closely related taxonomically or genetically (California Department of Fish and Game (CDFG) 2001, p. 473).

Biology

Nearly all information available on longfin smelt biology comes from either the Bay-Delta population or the Lake Washington population. Longfin smelt generally spawn in freshwater and then move downstream to brackish water to rear. The life cycle of most longfin smelt generally requires estuarine conditions (CDFG 2009, p. 1).

Bay-Delta Population

Longfin smelt are considered pelagic and anadromous (Moyle 2002, p. 236), although anadromy in longfin smelt is poorly understood, and certain populations are not anadromous and complete their entire life cycle in freshwater lakes and streams (see
Lake Washington Population
section below). Within the Bay-Delta, the term pelagic refers to organisms that occur in open water away from the bottom of the water column and away from the shore. Juvenile and adult longfin smelt have been found throughout the year in salinities ranging from pure freshwater to pure seawater, although once past the juvenile stage, they are typically collected in waters with salinities ranging from 14 to 28 parts per thousand (ppt) (Baxter 1999, pp. 189-192). Longfin smelt are thought to be restricted by high water temperatures, generally greater than 22 degrees Celsius (°C) (71 degrees Fahrenheit (°F)) (Baxter
et. al.
2010, p. 68), and will move down the estuary (seaward) and into deeper water during the summer months, when water temperatures in the Bay-Delta are higher. Within the Bay-Delta, adult longfin smelt occupy water at temperatures from 16 to 20 °C (61 to 68 °F), with spawning occurring in water with temperatures from 5.6 to 14.5 °C (41 to 58 °F) (Wang 1986, pp. 6-9).

Longfin smelt usually live for 2 years, spawn, and then die, although some individuals may spawn as 1- or 3-year-old fish before dying (Moyle 2002, p. 36). In the Bay-Delta, longfin smelt are believed to spawn primarily in freshwater in the lower reaches of the Sacramento River and San Joaquin River. Longfin smelt congregate in deep waters in the vicinity of the low salinity zone (LSZ) near X2 (see definition below) during the spawning period, and it is thought that they make short runs upstream, possibly at night, to spawn from these locations (CDFG 2009, p. 12; Rosenfield 2010, p. 8). The LSZ is the area where salinities range from 0.5 to 6 practical salinity units (psu) within the Bay-Delta (Kimmerer 1998, p. 1). Salinity in psu is determined by electrical conductivity of a solution, whereas salinity in parts per thousand (ppt) is determined as the weight of salts in a solution. For use in this document, the two measurements are essentially equivalent. X2 is defined as the distance in kilometers up the axis of the estuary (to the east) from the Golden Gate Bridge to the location where the daily average near-bottom salinity is 2 psu (Jassby
et al.
1995, p. 274; Dege and Brown 2004, p. 51).

Longfin smelt in the Bay-Delta may spawn as early as November and as late as June, although spawning typically occurs from January to April (CDFG 2009, p. 10; Moyle 2002, p. 36). Longfin smelt have been observed in their winter and spring spawning period as far upstream as Isleton in the Sacramento River, Santa Clara shoal in the San Joaquin system, Hog Slough off the South-Fork Mokelumne River, and in Old River south of Indian Slough (CDFG 2009a, p. 7; Radtke 1966, pp. 115-119).

Exact spawning locations in the Delta are unknown and may vary from year to year in location, depending on environmental conditions. However, it seems likely that spawning locations consist of the overlap of appropriate conditions of flow, temperature, and salinity with appropriate substrate (Rosenfield 2010, p. 8). Longfin smelt are known to spawn over sandy substrates in Lake Washington and likely prefer similar substrates for spawning in the Delta (Baxter
et. al.
2010, p. 62; Sibley and Brocksmith 1995, pp. 32-74). Baxter found that female longfin smelt produced between 1,900 and 18,000 eggs, with fecundity greater in fish with greater lengths (CDFG 2009, p. 11). At 7 °C (44.6 °F), embryos hatch in 40 days (Dryfoos 1965, p. 42); however, incubation time decreases with increased water temperature. At 8-9.5 °C (46.4-49.1 °F), embryos hatch at 29 days (Sibley and Brocksmith 1995, pp. 32-74).

Larval longfin smelt less than 12 millimeters (mm) (0.5 in) in length are buoyant because they have not yet developed an air bladder; as a result, they occupy the upper one-third of the water column. After hatching, they quickly make their way to the LSZ via river currents (CDFG 2009, p. 8; Baxter 2011a, pers comm.). Longfin smelt develop an air bladder at approximately 12-15 mm (0.5-0.6 in.) in length and are able to migrate vertically in the water column. At this time, they shift habitat and begin living in the bottom two-thirds of the water column (CDFG 2009, p. 8; Baxter 2008, p. 1).

Longfin smelt larvae can tolerate salinities of 2-6 psu within days of hatching, and can tolerate salinities up to 8 psu within weeks of hatching

(Baxter 2011a, pers. comm.). However, very few larvae (individuals less than 20 mm in length) are found in salinities greater than 8 psu, and it takes almost 3 months for longfin smelt to reach juvenile stage. A fraction of juvenile longfin smelt individuals are believed to tolerate full marine salinities (greater than 8 psu) (Baxter 2011a, pers. comm.).

Longfin smelt are dispersed broadly in the Bay-Delta by high flows and currents, which facilitate transport of larvae and juveniles long distances. Longfin smelt larvae are dispersed farther downstream during high freshwater flows (Dege and Brown 2004, p. 59). They spend approximately 21 months of their 24-month life cycle in brackish or marine waters (Baxter 1999, pp. 2-14; Dege and Brown 2004, pp. 58-60).

In the Bay-Delta, most longfin smelt spend their first year in Suisun Bay and Marsh, although surveys conducted by the City of San Francisco collected some first-year longfin in coastal waters (Baxter 2011c, pers. comm.; City of San Francisco 1995, no pagination). The remainder of their life is spent in the San Francisco Bay or the Gulf of Farallones (Moyle 2008, p. 366; City of San Francisco 1995, no pagination). Rosenfield and Baxter (2007, pp. 1587, 1590) inferred based on monthly survey results that the majority of longfin smelt from the Bay-Delta were migrating out of the estuary after the first winter of their life cycle and returning during late fall to winter of their second year. They noted that migration out of the estuary into nearby coastal waters is consistent with captures of longfin smelt in the coastal waters of the Gulf of Farallones. It is possible that some longfin smelt may stay in the ocean and not re-enter freshwater to spawn until the end of their third year of life (Baxter 2011d, pers. comm.). Moyle (2010, p. 8) states that longfin smelt that migrate out of and back into the Bay-Delta estuary may primarily be feeding on the rich planktonic food supply in the Gulf of Farallones. Rosenfield and Baxter (2007, p. 1290) hypothesize that the movement of longfin smelt into the ocean or deeper water habitat in summer months is at least partly a behavioral response to warm water temperatures found during summer and early fall in the shallows of south San Francisco Bay and San Pablo Bay (Rosenfield and Baxter 2007, p. 1590).

In the Bay-Delta, calanoid copepods such as
Pseudodiatomus forbesi
and
Eurytemora sp.,
as well as the cyclopoid copepod
Acanthocyclops vernali
(no common names), are the primary prey of longfin smelt during the first few months of their lives (approximately January through May) (Slater 2009b, slide 45). Copepods are a type of zooplankton (organisms drifting in the water column of oceans, seas, and bodies of fresh water). The longfin smelt's diet shifts to include mysids such as opossum shrimp (
Neomysis mercedis
) and other small crustaceans (
Acanthomysis
sp.) as soon as they are large enough (20-30 mm (0.78-1.18 in)) to consume these larger prey items, sometime during the summer months of the first year of their lives (CDFG 2009, p. 12). Upstream of San Pablo Bay, mysids and amphipods form 80-95 percent or more of the juvenile longfin smelt diet by weight from July through September (Slater 2009, unpublished data). Longfin smelt occurrence is likely associated with the occurrence of their prey, and both of these invertebrate groups occur near the bottom of the water column during the day under clear water marine conditions.

Lake Washington Population

The Lake Washington population near Seattle, Washington is considered a landlocked population of longfin smelt, as are the populations of longfin smelt in Harrison and Pitt Lakes in British Columbia east of Vancouver (Chigbu and Sibley 1994, p. 1). These populations are not anadromous and complete their entire life cycle in freshwater. Young longfin smelt feed primarily on the copepods
Diaptomus, Diaphanosoma,
and
Epischura,
with older fish switching over to mysids (Wydoski and Whitney 2003, p. 105). Chigbu and Sibley (1994, pp. 11-14) found that mysids dominate the diets of longfin smelt in their second year of life (age-1), while amphipods, copepods, and daphnia also contributed substantially to the longfin smelt's diet. A strong spawning run of longfin smelt occurs on even years in Lake Washington, with weak runs on odd years. They spawn at night in the lower reaches of at least five streams that flow into Lake Washington. Water temperatures during spawning were 4.4 °C (40 °F) to 7.2 °C (45 °F) (Wydoski and Whitney 2003, p. 105). Chigbu and Sibley (1994, p. 9) found that female longfin smelt produced between 6,000 and 24,000 eggs, while Wydoski and Whitney (2003, p. 105) found that longfin smelt produced between 1,455 and 1,655 eggs. The reason for the large difference between the observations of these two studies is not known.

Habitat

Longfin smelt have been collected in estuaries from the Bay-Delta (33° N latitude) to Prince William Sound (62° N latitude), a distance of approximately 1,745 nautical miles (Figure 1). Mean annual water temperatures range from 2.4 °C (36.3 °F) in Anchorage to 14.1 °C (57.3 °F) in San Francisco (NOAA 2011a). The different estuary types that the longfin smelt is found in and the range of variability of environments where the species has been observed will be discussed below.

BILLING CODE 4310-55-P

EP02AP12.000

The origin and geomorphology of West Coast estuaries result from geologic forces driven by plate tectonics and have been modified by glaciations and sea level rise (Emmett
et al.
2000, pp. 766-767). Major classifications of estuaries include fjord, drowned-river valley, lagoon, and bar-built. Fjords typically are long, narrow, steep-sided valleys created by glaciation, with moderately high freshwater inflow but little mixing with seawater due to the formation of a sill at the mouth (NOAA 2011b). Fjords generally have one large tributary river and numerous small streams (Emmett
et al.
2000, p. 768). Drowned-river valleys, also termed coastal plain estuaries, are found primarily in British Columbia, Washington, and Oregon, and are the dominant type along the west coast, occurring as a result of rising sea levels following the last ice age. Lagoons, primarily found in California, occur where coastal river systems that are closed to the sea by sand spits for much of the year are breached during the winter (Emmett
et al.
2000, p. 768). The rarest type of estuary is the bar-built, which is formed by a bar and semi-enclosed body of water (Emmett
et al.
2000, p. 768). Estuaries have also been classified by physical or environmental

variables into Northern Riverine, Southern California, Northern Estuarine, Central Marine, Fjord, and Coastal Northwest Groups (Monaco
et al.
1992, p. 253). Longfin smelt have been collected from estuaries of all types and classifications.

The Bay-Delta is the largest estuary on the West Coast of the United States (Sommer
et al.
2007, p. 271). The modern Bay-Delta bears only a superficial resemblance to the historical Bay-Delta. The Bay-Delta supports an estuary covering approximately 1,235 square kilometers (km
2
) (477 square miles (mi
2
)) (Rosenfield and Baxter 2007, p. 1577), which receives almost half of California's runoff (Lehman 2004, p. 313). The historical island marshes surrounded by low natural levees are now intensively farmed and protected by large, manmade structures (Moyle 2002, p. 32). The watershed, which drains approximately 40 percent of the land area of California, has been heavily altered by dams and diversions, and nonnative species now dominate, both in terms of numbers of species and numbers of individuals (Kimmerer 2004, pp. 7-9). The Bay Institute has estimated that intertidal wetlands in the Delta have been diked and leveed so extensively that approximately 95 percent of the 141,640 hectares (ha) (350,000 acres (ac)) of tidal wetlands that existed in 1850 are gone (The Bay Institute 1998, p. 17).

The physical and biological characteristics of the estuary define longfin smelt habitat. The Bay-Delta is unique in that it contains significant amounts of tidal freshwater (34 km
2
(13 mi
2
)) and mixing zone (194 km
2
(75 mi
2
)) habitat (Monaco
et al.
1992, pp. 254-255, 258). San Francisco Bay is relatively shallow and consists of a northern bay that receives freshwater inflow from the Sacramento-San Joaquin system and a southern bay that receives little freshwater input (Largier 1996, p. 69). Dominant fish species are highly salt-tolerant and include the commercially important Pacific sardine (
Sardinops sagax
) and rockfish (
Sebastes
spp.). Major habitat types include riverine and tidal wetlands, mud flat, and salt marsh, with substantial areas of diked wetland managed for hunting. The sandy substrates that longfin smelt are presumed to use for spawning are abundant in the Delta.

The Russian River collects water from a drainage area of approximately 3,846 km
2
(1,485 mi
2
), has an average annual discharge of 1.6 million acre-feet, and is approximately 129 km (80 mi) in length (Langridge
et al.
2006, p. 4). Little information is available on potential spawning and rearing habitat for longfin smelt, but it is likely to be both small and ephemeral because spawning and rearing habitat is highly dependent upon freshwater inflow, and there may be insufficient freshwater flows for spawning and rearing in some years (Moyle 2010, p. 5). A berm encloses the mouth of the Russian River during certain times of the year, essentially cutting it off from the coastal ocean. This results in a lack of connectivity with the ocean that could be important during dry years. However, in most years the berm is breached by freshwater flows, which allows longfin smelt to enter the Russian River and spawn.

The Eel River drains an area of 3,684 mi
2
(9,542 km
2
) and is the third largest river in California. Wetlands and tidal areas have been reduced 60 to 90 percent since the 1800s (Cannata and Hassler 1995, p. 1), resulting in changes in tidal influence and a reduction in channel connectivity (Downie 2010, p. 15). The estuary is characterized by a small area where freshwater and saltwater mix (Monaco
et al.
1992, p. 258) and thus provides only limited potential longfin rearing habitat.

Humboldt Bay is located only 26 km (16 mi) north of the Eel River and is approximately 260 mi (418 km) north of the Bay-Delta. Humboldt Bay is the second largest coastal estuary in California after the Bay-Delta. However, true estuarine conditions rarely occur in Humboldt Bay because it receives limited freshwater input and experiences little mixing of freshwater and saltwater (Pequegnat and Butler 1982, p. 39).

The Klamath Basin has been extensively modified by levees, dikes, dams, and the draining of natural water bodies since the U.S. Bureau of Reclamation's Klamath Project, designed to improve the region's ability to support agriculture, began in 1905. These changes to the system have altered the biota of the basin (NRC 2008, p. 16). Over the years, loss of thousands of acres of connected wetlands and open water in the Klamath River Basin has greatly reduced habitat value, likely depleting the ability of this area to cycle nutrients and affecting water quality (USFWS 2008, p. 55). The river drains a vast area of 10 million ac (4 million ha). Although a large river, the Klamath River estuary is characterized by small tidal freshwater and mixing zones (Monaco
et al.
1992, p. 258) and thus provides limited potential longfin smelt rearing habitat.

Yaquina Bay is located on the mid-coastal region of Oregon, 201 km (125 mi) south of the Columbia River and 348 km (216 mi) north of the California border. Wetlands encompass 548 ha (1,353 ac), including 216 ha (534 ac) of mud flats and 331 ha (819 ac) of tidal marshes (Yaquina Bay Geographic Response Plan 2005, p. 2.1). Forty-eight percent of the estuary is intertidal (Brown
et al.
2007, p. 6). The estuary has been modified greatly, being alternately dredged and filled at different locations as a result of development. Dredging, industrial, and residential uses have reduced fish habitat and water quality in the bay. Dredging disturbs sediment, resulting in increased turbidity and reduced sunlight penetration, which can impact native eelgrasses and the benthic species dependent eelgrass beds for breeding, spawning, and shelter (Oberrecht 2011, pp. 1-8).

On the Columbia River, dams, dikes, maintenance dredging, and urbanization have all contributed to habitat loss and alterations that have negatively affected fish and wildlife populations (Lower Columbia River Estuary Partnership 2011, p. 1). It is estimated that as much as 43 percent of estuarine tidal marshes and 77 percent of tidal swamps in the river estuary available for fish species have been lost since 1870 (Columbia River Estuary Study Taskforce 2006, pp. 1-30). Sixty square miles of peripheral tidal habitat have been lost to diking, filling, and conversion to upland habitat for industrial and agricultural use since 1870 (Columbia River Estuary Study Taskforce 2006, p. 1). Prior to construction of dams, estuary islands and much of the floodplain were inundated throughout the year, beginning in December and again in May or June. Dam operations on the Columbia River's main stem and major tributaries have substantially reduced peak river flows. Dikes and levees have all but eliminated flooding in many low-lying areas. Dredging of shipping channels has caused loss of wetlands and altered shoreline configuration. Dredging has resulted in large sediment reductions upstream, and the dredged sediments have created islands downstream. This has likely reduced spawning habitat and sheltering sites for fish (OWJP 1991, pp. 1-24; Lower Columbia Fish Recovery Board 2004a, pp. 1-192).

Puget Sound is a large saltwater estuary of interconnected flooded glacial valleys located at the northwest corner of the State of Washington. Puget Sound is about 161 km (100 mi) long, covers about 264,179 ha (652,800 ac), and has over 2,092 km (1,300 mi) of shoreline. Fed by streams and rivers from the Olympic and Cascade Mountains, waters flow out to the

Pacific Ocean through the Strait of Juan de Fuca (Lincoln 2000, p. 1). The basin consists of eight major habitat types, the largest of which is kelp and eelgrass, but also includes wetlands, mudflats, and sandflats. Puget Sound consists of five regions, each with its own physical and biological characteristics. Urban and industrial development borders the main basin, which is bounded by Port Townsend on the north and the Narrows (Tacoma) on the south. Approximately 30 percent of freshwater inflow to the main basin is from the Skagit River, which drains an area of approximately 8,011 km
2
(3,093 mi
2
). Sills at Admiralty Inlet and the Narrows influence circulation. Puget Sound is highly productive. The fish community includes many commercially important species, such as Pacific herring, Pacific salmon, and several species of rockfish (NOAA 2011c, p. 11). There are 10 major dams and thousands of small water diversions in the Puget Sound system (Puget Sound Partnership 2008b, p. 21). Human activities in the region have resulted in the loss of 75 percent of the saltwater marsh habitat and 90 percent of the estuarine and riverine wetlands (Puget Sound Partnership 2008b, p. 21).

The coastline of British Columbia has been shaped by plate tectonics and extensive glaciations. Particularly in summer, prevailing winds drive coastal upwelling, which results in a highly productive food chain. The tidal amplitude is 3-5 meters (m) (9.8-16.4 ft) in most areas, and numerous large and small rivers provide freshwater inflow. Biological communities are diverse and highly variable, including coastal wetlands, kelp beds, and seaweed beds that support a diverse marine fauna (Dale 1997, pp. 13-15). Nearshore areas of British Columbia are characterized by steep to moderately sloping fjords, 20-50 m (65-164 ft) in depth, with salinities ranging from 18 to 28 ppt (AXYS Environmental Consulting 2001, pp. 5, 11, 20). Bar-built estuaries that are semi-enclosed by an ocean-built bar occur on the west coast of Vancouver Island and the Queen Charlotte Islands (Emmett
et al.
2000, pp. 769-770). Oxygen depletion is common in fjords (Emmett
et al.
2000, p. 776), but because they are anadromous, longfin smelt would presumably be able to avoid those conditions. However, if depletion were to occur during spawning or rearing, recruitment could be affected.

The Fraser River, at approximately 1,375 miles (2,213 km), is the longest river in British Columbia and the tenth longest river in Canada. The Fraser River drains an area of 220,000 km
2
and flows to the Strait of Georgia at the City of Vancouver before it drains into the Pacific Ocean. Diking and drainage in the lower basin area have reduced the extent of estuarine wetlands that are important to the longfin smelt and other fishes that utilize these areas (Blomquist 2005, p. 8).

Habitat types common in Alaskan estuaries include eel grass beds, understory kelp, sand and gravel beds, and bedrock outcrops (NOAA 2011d). Shallow nearshore areas provide a mosaic of habitat types that support a variety of fishes (NOAA 2005, p. 59). In southwestern Alaska, the related osmerid species capelin (
Mallotus villosus
) was found to occur in sand-and-gravel habitats, and the surf smelt (
Hypomesus pretiosus
) was found to occur in bedrock habitats (NOAA 2005, pp. 27, 29). As in British Columbia, if oxygen depletion occurs in fjord habitats during spawning or rearing, longfin smelt recruitment could be affected.

Cook Inlet is a large mainland Alaskan estuary located in the northern Gulf of Alaska. Cook Inlet is approximately 290 km (180 miles) long. The watershed covers about 100,000 km
2
of southern Alaska (USACE 2011, p. 1).

Distribution

Longfin smelt are widely distributed along 3,541 km (2,200 mi) of Pacific coastline from the Bay-Delta to Cook Inlet, Alaska (Table 1). We found no evidence of range contraction; the current distribution of longfin smelt appears to be similar to its historical distribution.

Table 1—Known Occurrences of Longfin Smelt

State
Location
Reference

California
Monterey Bay
Eschmeyer 1983, p. 82; Wang 1986, pp. 6-10).

Bay-Delta
Eschmeyer 1983, p. 82; Wang 1986, pp. 6-10.

Offshore Bay-Delta
City of San Francisco 1993, p. 5-8.

Russian River Estuary
Cook 2010, pers. comm.

Van Duzen River
Moyle 2002, p. 235.

McNulty Slough of Eel River
CDFG 2010, unpublished data.

Offshore Humboldt Bay
Quirollo 1994, pers. comm.

Humboldt Bay and tributaries
CDFG 2010, unpublished data.

Mad River
Moyle 2002, p. 235.

Klamath River

Kisanuki
et al.
1991, p. 72, CDFG 2009, p. 5.

Lake Earl

D. McLeod field note 1989
(Cannata and Downie 2009).

Oregon
Coos Bay
Veroujean 1994, p. 1.

Yaquina Bay
ODFW 2011, pp. 1-3, ANHP 2006, p. 3.

Tillamook Bay
Ellis 2002, p. 17.

Columbia River Estuary
ODFW 2011, pp. 1-3.

Washington
Willapa Bay
WDFW 2011, pp. 1-3.

Grays Harbor
U.S. Army Corps of Engineers 2000, p. 2.

Puget Sound Basin
Miller and Borton 1980, p. 17.4.

Lake Washington
Chigbu and Sibley 1994, p. 1.

British Columbia
Fraser River
Fishbase 2011a, p. 1; Fishbase 2011b, p. 1.

Pitt Lake
Taylor 2011, pers. comm.

Harrison Lake
Page and Burr 1991, p. 57.

Vancouver
Hart 1973, p. 147.

Prince Rupert
Hart 1973, p. 147.

Skeena Estuary
Kelson 2011, pers. comm.

Alaska
Dixon Entrance
Alaska Natural Heritage Program 2006, p. 3.

Sitka National Historical Park
NPS 2011, p. 1.

Glacier Bay
Arimitsu 2003, pp. 35, 41.

Klondike Gold Rush National Historical Park
NPS 2011, p. 1.

Yakutat Bay
Alaska Natural Heritage Program 2006, p. 3.

Wrangell-St. Elias National Park
Arimitsu 2003, pp. 35, 41, NPS 2011, p. 1.

Cook Inlet
NOAA 2010b, p. 4, NOAA 2010a, p. 8.

Kachemak Bay

Abookire
et al.
2000, NPS 2011, p. 1.

Hinchinbrook Island
Alaska Natural Heritage Program 2006, p. 3.

Lake Clark National Park and Preserve
NPS 2011, p. 1.

Prince William Sound
Alaska Natural Heritage Program 2006, p. 3.

California

The southernmost known population of longfin smelt is the Bay-Delta estuary, and longfin smelt occupy different habitats of the estuary at various stages in their life cycle (See Habitat section above). Eschmeyer (1983, p. 82) reported the southern extent of the range as Monterey Bay, and Wang (1986, pp. 6-10) reported that an individual longfin smelt had been captured at Moss Landing in Monterey Bay in 1980. Most sources, however, identify the Bay-Delta as the southern extent of the species' range (Moyle 2002, p. 235).

Small numbers of longfin were collected within the Russian River estuary each year between 1997 and 2000 (SCWA 2001, p. 18). No surveys were conducted in 2001 or 2002 (Cook 2011, pers. comm.). Recent surveys (since 2003) in the Russian River estuary conducted by Sonoma County Water Agency have not collected longfin smelt; however, in 2003, trawling surveys were replaced by beach seining, a type of survey less likely to capture a pelagic fish species such as the longfin smelt. Longfin smelt breeding has not been documented at the Russian River (Baxter 2011b, pers. comm.), and because of its limited size, the Russian River estuary is not believed to be capable of supporting a self-sustaining longfin smelt population (The Bay Institute
et al.
2007, p. ii; Moyle 2010, p. 5).

Longfin smelt were observed spawning in the Eel River estuary in 1974 (Puckett 1977, p. 19). Although longfin were observed in the Eel River in 2008 and 2009 (Cannata and Downie 2009), it is unknown whether or not they currently spawn there. Humboldt Bay is located 420 km (260 mi) north of the Bay-Delta. Longfin smelt were collected in Humboldt Bay or its tributaries every year from 2003 to 2009, with the exception of 2004 (CDFG 2010, unpublished data). Longfin smelt also have been observed in coastal waters adjacent to Humboldt Bay (Quirollo 1994, pers. comm.). The Humboldt Bay population is thought to be the nearest known breeding population to the Bay-Delta (Baxter 2011b, pers. comm.). Longfin smelt were collected consistently in the Klamath River estuary between 1979 and 1989 (Kisanuki
et al.
1991, p. 72), and one longfin smelt was collected in the Klamath River in 2001 (CDFG 2009, p. 5).

Oregon

In Oregon, there are historical records of longfin smelt in Tillamook Bay, Columbia River, Coos Bay, and Yaquina Bay (ANHP 2006, p. 3). One individual was detected in Tillamook Bay in 2000 (Ellis 2002, p. 17). Williams
et al.
(2004, p. 30) collected 308 longfin in the Columbia River estuary in 2004. Longfin smelt were reported in the Columbia River estuary, the coastal waters adjacent to the Columbia River, and in Yaquina Bay in 2009 (Nesbit 2011, pers. comm.). In Coos Bay, longfin smelt were detected in low numbers in the early 1980s. However, longfin smelt do not appear to be common in Coos Bay and were not detected during sampling that occurred in the 1970s and the late 1980s (Veroujean 1994, no pagination).

Washington

In Washington, within the Puget Sound Basin, longfin smelt are known to occur in the Nooksack River, Bellingham Bay, Snohomish River, Duwamish River, Skagit Bay, Strait of San Juan de Fuca, Twin River, and Pysht River (Table 1). Longfin smelt are known to occur in nearby Bellingham Bay (Penttila 2007, p. 4). Longfin smelt were collected in the Snohomish River estuary during extensive beach seine and fyke trapping in 2009 (Rice 2010, pers. comm.). Longfin smelt were captured (reported as non-target) in high-rise otter trawls in the lower Duwamish River (Anchor and King County 2007, p. 11). Longfin smelt are common in the Strait of San Juan de Fuca (Penttila 2007, p. 4). Miller
et al.
(1980, p. 28) found longfin smelt to be the second most common species in tow-net surveys conducted in the Strait of San Juan de Fuca. Most fish caught in these surveys were young of the year and were found near the Twin and Pysht Rivers, both of which may have suitable spawning grounds (Miller
et al.
1980, p. 28). Occurrences of longfin smelt within northern Puget Sound and the Strait of Georgia may reflect the abundance and distribution of the anadromous populations from the Fraser River in British Columbia (Washington Department of Fish and Wildlife 2011, pp. 1-3). Currently, the National Park Service states that longfin smelt are probably present within Olympic National Park (NPS 2011, p. 1). Longfin smelt appear to be common in Grays Harbor (U.S. Army Corps of Engineers 2000, p. 2). Longfin smelt have been infrequently documented in the upper Chehalis estuary at Cosmopolis; however, when they do occur, they have been reported as abundant (Anderson 2011). Ocean trawls off Willapa Bay have collected longfin smelt, although no spawning population has been identified in the basin (Anderson 2011).

A resident, freshwater population of longfin smelt occurs in Lake Washington (Chigbu and Sibley 1994, p. 1). First caught in 1959, it is believed that the longfin smelt either were introduced to the lake or became trapped during canal construction (Chigbu
et al.
1998, p. 180). In the 1960s, the abundance of longfin smelt in Lake Washington was low but increased to higher levels in the 1980s (Chigbu and Sibley 1994, p. 4).

British Columbia

Longfin smelt populations occur in Pitt Lake and Harrison Lake in British Columbia (Page and Burr 1991, p. 57; Taylor 2011, pers. comm.); these populations are believed to be resident fish that are not anadromous (that is, they are thought to complete their entire life cycle in freshwater). Pitt Lake is located approximately 64 river km (40 mi) up the Fraser and Pitt Rivers, and Harrison Lake is located approximately 121 river km (75 mi) up the Fraser and Harrison Rivers. Longfin smelt are known to occur within the Fraser River near Vancouver (Hart 1973, p. 147; Fishbase 2011a, p. 1; Fishbase 2011b, p. 1). Longfin smelt are also known to occur in the Skeena River estuary near

Prince Rupert (Hart 1973, p. 147; Kelson 2011, pers. comm.; Gottesfeld 2002, p. 54).

Alaska

In Alaska, longfin smelt are known from Hinchinbrook Island, Prince William Sound, Dixon Entrance, Yakutat Bay, and Cook Inlet (Alaska Natural Heritage Program 2006, p. 3). In nearly 1,000 recent beach seine surveys in Alaska, longfin smelt have only been caught off Fire Island in upper Cook Inlet in 2009 and 2010 (NOAA 2010b, p. 4; Johnson 2010, pers. comm.; Wing 2010, pers. comm.). However, as stated earlier, longfin smelt are unlikely to be caught in beach seine surveys because they are a pelagic species and do not typically occur near shore where beach seine surveys take place. Surveys in Prince William Sound did not collect longfin smelt in 2006 or 2007 (NOAA 2011, p. 1). Longfin smelt were collected in Wrangell-St. Elias National Park and Glacier Bay in 2001 and 2002 (Arimitsu 2003, pp. 35, 41). Longfin were collected in Kachemak Bay in 1996-1998 seine and trawling surveys (Abookire
et al.
2000). The NPS was not able to confirm presence or absence in Lake Clark National Park and Preserve. The NPS concludes that presence is probable in Glacier Bay National Park and Preserve, Klondike Gold Rush National Historical Park, Sitka National Historical Park, and Wrangell-St. Elias National Park and Preserve (NPS 2011, p. 1).

Abundance

In most locations throughout their range, longfin smelt populations have not been monitored. Within the Bay-Delta, longfin smelt are consistently collected in the monitoring surveys that have been conducted by CDFG as far back as the late 1960s. We know of no similar monitoring data for other longfin smelt populations. CDFG did report catches of longfin smelt in Humboldt Bay from surveys conducted between 2003 and 2009; small numbers of longfin were collected each of the years except 2004 (CDFG 2010, unpublished data). Moyle (2002, p. 237; 2010, p. 4) noted that the longfin smelt population in Humboldt Bay appeared to have declined between the 1970s and 2002, but survey data are not available from that time.

Longfin smelt numbers in the Bay-Delta have declined significantly since the 1980s (Moyle 2002, p. 237; Rosenfield and Baxter 2007, p. 1590; Baxter
et. al.
2010, pp. 61-64). Rosenfield and Baxter (2007, pp. 1577-1592) examined abundance trends in longfin smelt using three long-term data sets (1980-2004) and detected a significant decline in the Bay-Delta longfin smelt population. They confirmed the positive correlation between longfin smelt abundance and freshwater flow that had been previously documented by others (Stevens and Miller 1983, p. 432; Baxter
et al.
1999, p. 185; Kimmerer 2002b, p. 47), noting that abundances of both adults and juveniles were significantly lower during the 1987-1994 drought than during either the pre- or post-drought periods (Rosenfield and Baxter 2007, pp. 1583-1584).

Despite the correlation between drought and low population in the 1980s and 90s, the declines in the first decade of this century appear to be caused in part by additional factors. Abundance of longfin smelt has remained very low since 2000, even though freshwater flows increased during several of these years (Baxter
et al.
2010, p. 62). Abundance indices derived from the Fall Midwater Trawl (FMWT), Bay Study Midwater Trawl (BSMT), and Bay Study Otter Trawl (BSOT) all show marked declines in Bay-Delta longfin smelt populations from 2002 to 2009 (Messineo
et al.
2010, p. 57). Longfin smelt abundance over the last decade is the lowest recorded in the 40-year history of CDFG's FMWT monitoring surveys. Scientists became concerned over the simultaneous population declines since the early 2000s of longfin smelt and three other Bay-Delta pelagic fish species—delta smelt (
Hypomesus transpacificus
), striped bass (
Morone saxatilis
), and threadfin shad (
Dorosoma petenense
) (Sommer
et al.
2007, p. 273). The declines of longfin smelt and these other pelagic fish species in the Bay-Delta since the early 2000s has come to be known as the Pelagic Organism Decline, and considerable research efforts have been initiated since 2005, to better understand causal mechanisms underlying the declines (Sommer
et al.
2007, pp. 270-277; MacNally
et al.
2010, pp. 1417-1430; Thomson
et al.
2010, pp. 1431-1448). The population did increase in the 2011 FMWT index to 477 (Contreras 2011, p. 2), probably a response to an exceptionally wet year.

The FMWT index of abundance in the Bay-Delta shows great annual variation in abundance but a severe decline over the past 40 years (Figure 2). The establishment of the overbite clam (
Corbula amurensis
) in the Bay-Delta in 1987 is believed to have contributed to the population decline of longfin smelt (See Factor E: Introduced Species, below), as well as to the declining abundance of other pelagic fish species in the Bay-Delta (Sommer
et al.
2007, p. 274). Figure 2 shows low values of the abundance index for longfin smelt during drought years (1976-1977 and 1986-1992) and low values overall since the time that the overbite clam became established in the estuary.

EP02AP12.001

Using data from 1975-2004 from the FMWT survey, Rosenfield and Baxter 2007 (p. 1589) found that longfin smelt exhibit a significant stock-recruitment relationship—abundance of juvenile (age-0) fish is directly related to the abundance of adult (age-1) fish from the previous year. They found that the abundance of juvenile fish declined by 90 percent during the time period analyzed. Rosenfield and Baxter (2007, p. 1589) also found a decline in age-1 individuals that was significant even after accounting for the decline in the age-0 population. If unfavorable environmental conditions persist for one or more years, recruitment into the population could be suppressed, affecting the species' ability to recover to their previous abundance. The current low abundance of adult longfin smelt within the Bay-Delta could reduce the ability of the species to persist in the presence of various threats.

Conservation Actions

Bay-Delta

The CALFED program existed as a multi-purpose (water supply, flood protection, and conservation) program with significant ecosystem restoration and enhancement elements. Implemented by the California Bay-Delta Authority, the program brought together more than 20 State and Federal agencies to develop a long-term comprehensive plan to restore ecological health and improve water management for all beneficial uses in the Bay-Delta system. The program specifically addressed ecosystem quality, water quality, water supply, and levee system integrity. The California Bay-Delta Authority was replaced in 2009 by the Delta Stewardship Council, but many of its programs continue to be implemented and are now housed within the CALFED program's former member agencies.

The CALFED Ecosystem Restoration Program (ERP) developed a strategic plan for implementing an ecosystem-based approach for achieving conservation targets (CALFED 2000a, pp. 1-3). The CDFG is the primary implementing agency for the ERP. The goal of ERP in improving conditions for longfin smelt will carry forward, irrespective of the species Federal listing status. CALFED had an explicit goal to balance the water supply program elements with the restoration of the Bay-Delta and tributary ecosystems and recovery of the longfin smelt and other species. Because achieving the diverse goals of the program is iterative and subject to annual funding by diverse agencies, the CALFED agencies have committed to maintaining balanced implementation of the program within an adaptive management framework. The intention of this framework is that the storage,

conveyance, and levee program elements would be implemented in such a way that the longfin smelt's status would be maintained and eventually improved.

CALFED identified 54 species enhancement conservation measures for longfin smelt, more than half of which have been completed (CALFED Ecosystem Restoration Project 2011, entire). One such restoration action at Liberty Island at the southern end of the Yolo Bypass (a flood control project) has likely benefitted longfin smelt. After years of active agricultural production on Liberty Island, the levees were breached in 1997, and the island was allowed to return to a more natural state (Wilder 2010, slide 4). Wildlands Corporation has recently completed a restoration project removing several levees surrounding Liberty Island and creating 186 acres of various habitats for fish (Wildlands 2011, p. 1). Longfin smelt are utilizing the flooded island, and were collected in a number of surveys between 2003 and 2005 (Liberty Island Monitoring Program 2005, pp. 42-44; Marshall
et al.
2006, p. 1).

The Bay-Delta Conservation Plan (BDCP), an effort to help provide restoration of the Bay-Delta ecosystem and reliable water supplies, is currently in preparation by a collaborative of water agencies, resource agencies, and environmental groups. The BDCP is intended to provide a basis for permitting take of listed species under sections 7 and 10 of the Act and the California Natural Communities Conservation Planning Act, and would provide a comprehensive habitat conservation and restoration plan for the Bay-Delta, as well as a new funding source. The BDCP shares many of the same goals outlined in the 2000 CALFED Record of Decision (CALFED 2000) but would not specifically address all listed-species issues. The BDCP would, however, target many of the threats to current and future listed species and could contribute to species recovery. However, the BDCP, if completed, would not be initiated until at least 2013 or later. The plan's implementation is anticipated to extend through 2060.

Humboldt Bay

The Humboldt Bay Watershed Advisory Committee has completed the Humboldt Bay Salmon and Steelhead Conservation Plan with funding from CDFG, National Oceanographic Atmospheric Administration (NOAA), and the California State Coastal Conservancy with the purpose of protecting and restoring salmon habitat in Humboldt Bay through cooperative planning (Humboldt Bay Watershed Advisory Committee 2005, pp. 1-2). Many of the habitat restoration activities proposed may benefit longfin smelt, including restoration in freshwater streams and brackish sloughs. The Natural Resource Services has designed an enhancement program that is based on the Humboldt Bay Salmon and Steelhead Conservation Plan. Natural Resource Services has completed a tidal marsh enhancement project on Freshwater Creek and has other projects in the design stage (Don Allen 2011, pers. comm.). The Natural Resource Services is a division of the Redwood Community Action Agency dedicated to improving the health of northern California communities and the watersheds that they depend on (NRS 2011, p. 1). These types of restoration efforts are current and ongoing and may benefit longfin smelt by increasing access to intertidal areas within Humboldt Bay.

Puget Sound

The Puget Sound Partnership is a Washington State Agency created in 2007, to oversee the restoration and protection of Puget Sound. The Puget Sound Partnership created an Action Agenda that identifies and prioritizes work needed to protect and restore Puget Sound (Puget Sound Partnership 2008b, p. 2). Protection actions including local watershed planning, shoreline management planning, and citizen involvement through groups such as beach watchers and shore stewards are among the current restoration efforts in Puget Sound watershed (Puget Sound Partnership 2008a, pp. 1-2). These measures are expected to benefit longfin smelt by protecting and restoring habitat through legislative approval and funding for land acquisition for protection and restoration of ecologically important lands and habitats and by adding lands to State Aquatic Reserves program (Puget Sound Partnership 2008a, pp. 1-2).

Alaska

State and Federal land ownership affords protection for vast distances of shoreline within Glacier Bay and Wrangell-St. Elias National Parks, Tongass National Forest, and State landholdings. Kachemak Bay, located near the mouth of lower Cook Inlet, is a National Estuarine Research Reserve regarded as extremely important for marine biodiversity conservation (ADFG 2006, pp. 133-134). Alaska's only State wilderness park, Kachemak Bay State Park, is also located in Kachemak Bay (ADNR 2011, p. 1). Yakutat Bay lies between peninsular and mainland Alaska and is bordered by Wrangell-St. Elias National Park to the northwest and Tongass National Forest. The Federal lands surrounding Yakutat Bay protect it from the effects of development. The Tongass National Forest management plan requires that logging activities be distanced from estuarine and riparian edges (ADFG 2006, p. 107). As a species group, the osmerids are identified in Alaska's Comprehensive Wildlife Conservation Strategy as Species of Greatest Conservation Need (ADFG 2006, pp. 140-143). The Conservation Action Plan for anadromous smelts identifies objectives, issues, and conservation actions to address information gaps. Determining life history, trophic ecology, instream flow and habitat needs, and monitoring protocols are included as measures that need to be undertaken as part of Alaska's Conservation Strategy to identify conservation status and needs of anadromous smelt including longfin.

Summary of Information Pertaining to the Five Factors

Section 4 of the Act (16 U.S.C. 1533) and implementing regulations (50 CFR part 424) set forth procedures for adding species to, removing species from, or reclassifying species on the Federal Lists of Endangered and Threatened Wildlife and Plants. Under section 4(a)(1) of the Act, a species may be determined to be endangered or threatened based on any of the following five factors:

(A) The present or threatened destruction, modification, or curtailment of its habitat or range;

(B) Overutilization for commercial, recreational, scientific, or educational purposes;

(C) Disease or predation;

(D) The inadequacy of existing regulatory mechanisms; or

(E) Other natural or manmade factors affecting its continued existence.

In making these findings, information pertaining to each species in relation to the five factors provided in section 4(a)(1) of the Act is discussed below. In considering what factors might constitute threats to a species, we must look beyond the exposure of the species to a particular factor to evaluate whether the species may respond to the factor in a way that causes actual impacts to the species. If there is exposure to a factor and the species responds negatively, the factor may be a threat, and during the status review, we attempt to determine how significant a threat it is. The threat is significant if it drives or contributes to the risk of extinction of the species such that the species warrants listing as

endangered or threatened as those terms are defined by the Act. However, the identification of factors that could impact a species negatively may not be sufficient to compel a finding that the species warrants listing. The information must include evidence sufficient to suggest that the potential threat has the capacity (i.e., it should be of sufficient magnitude and extent) to affect the species' status such that it meets the definition of endangered or threatened under the Act.

In making our 12-month finding on the petition, we considered and evaluated the best available scientific and commercial information. Much of the scientific and commercial information available on potential threats to longfin smelt comes from information on the Bay-Delta, and therefore the threats analysis is largely focused on the Bay-Delta longfin smelt population.

Factor A. The Present or Threatened Destruction, Modification, or Curtailment of Its Habitat or Range

Potential threats to longfin smelt habitat include the effects of reduced freshwater flow, climate change, and channel disturbance. Nearly all information available on Factor A threats to longfin smelt come from the Bay-Delta estuary. Therefore, our analysis below focuses on habitat impacts to the Bay-Delta population.

Reduced Freshwater Flow

Most longfin smelt populations, other than those in a few freshwater lakes in Washington and British Columbia, are known from estuaries. Estuaries are complex ecosystems with boundaries between freshwater, brackish water, and saltwater that vary in time and space. Drought and water diversions affect these boundaries by altering the amounts and timing of freshwater flow into and within the estuary. These altered freshwater flows affect the physical and biological characteristics of the estuary, and the physical and biological characteristics of the estuary define longfin smelt habitat.

Many environmental attributes respond to variance in freshwater flow into the estuary, including patterns of flooding and drought, nutrient loading, sediment loading (turbidity), concentration of organic matter and planktonic biota, physical changes in the movement and compression of the salt field, and changes in the hydrodynamic environment (Kimmerer 2002a, p. 40). The San Francisco Estuary exhibits one of the strongest and most consistent responses of biota to flow among large estuaries (Kimmerer 2004, p. 14).

Reduced freshwater flows into estuaries may affect fish and other estuarine biota in multiple ways. Effects may include: (1) Decreased nutrient loading, resulting in decreased primary productivity; (2) decreased stratification of the salinity field, resulting in decreased primary productivity; (3) decreased organic matter loading and deposition into the estuary; (4) reduced migration cues; (5) decreased sediment loading and turbidity, which may affect both feeding efficiency and predation rates; (6) reduced dilution of contaminants; (7) impaired transport to rearing areas (e.g., low-salinity zones); and (8) reduction in physical area of, or access to, suitable spawning or rearing habitat (Kimmerer 2002b, p. 1280).

Bay-Delta Population

Freshwater flow is strongly related to the natural hydrologic cycles of drought and flood. In the Bay-Delta estuary, increased Delta outflow during the winter and spring is the largest factor positively affecting longfin smelt abundance (Stevens and Miller 1983, pp. 431-432; Jassby
et al.
1995; Sommer
et al.
2007, p. 274; Thomson
et al.
2010, pp. 1439-1440). During high outflow periods, larvae presumably benefit from increased transport and dispersal downstream, increased food production, reduced predation through increased turbidity, and reduced loss to entrainment due to a westward shift in the boundary of spawning habitat and strong downstream transport of larvae (CFDG 1992; Hieb and Baxter 1993; CDFG 2009a). Conversely, during low outflow periods, negative effects of reduced transport and dispersal, reduced turbidity, and potentially increased loss of larvae to predation and increased loss at the export facilities result in lower young-of-the-year recruitment. Despite numerous studies of longfin smelt abundance and flow in the Bay-Delta, the underlying causal mechanisms are still not fully understood (Baxter
et al.
2010, p. 69; Rosenfield 2010, p. 9).

As California's population has grown, demands for reliable water supplies and flood protection have grown. In response, State and Federal agencies built dams and canals, and captured water in reservoirs, to increase capacity for water storage and conveyance resulting in one of the largest manmade water systems in the world (Nichols
et al.
1986, p. 569). Operation of this system has altered the seasonal pattern of freshwater flows in the watershed. Storage in the upper watershed of peak runoff and release of the captured water for irrigation and urban needs during subsequent low flow periods result in a broader, flatter hydrograph with less seasonal variability in freshwater flows into the estuary (Kimmerer 2004, p. 15).

In addition to the system of dams and canals built throughout the Sacramento River-San Joaquin River basin, the Bay-Delta is unique in having a large water diversion system located within the estuary (Kimmerer 2002b, p. 1279). The State Water Project (SWP) and Central Valley Project (CVP) operate two water export facilities in the Delta (Sommer
et al.
2007, p. 272). Project operation and management is dependent upon upstream water supply and export area demands. Despite the size of the water storage and diversion projects, much of the interannual variability in Delta hydrology is due to variability in precipitation from year to year. Annual inflow from the watershed to the Delta is strongly correlated to unimpaired flow (runoff that would hypothetically occur if upstream dams and diversions were not in existence), mainly due to the effects of high-flow events (Kimmerer 2004, p. 15). Water operations are regulated in part by the California State Water Resources Control Board (SWRCB) according to the Water Quality Control Plan (WQCP) (SWRCB 2000, entire). The WQCP limits Delta water exports in relation to Delta inflow (the Export/Inflow, or E/I ratio).

It is important to note that in the case of the Bay-Delta, freshwater flow is expressed as both Delta inflow (from the rivers into the Delta) and as Delta outflow (from the Delta into the lower estuary), which are closely correlated, but not equivalent. Freshwater flow into the Delta affects the location of the low salinity zone and X2 within the estuary. Because longfin smelt spawn in freshwater, they must migrate farther upstream to spawn as flow reductions alter the position of X2 and the low-salinity zone moves upstream (CDFG 2009, p. 17). Longer migration distances into the Bay-Delta make longfin smelt more susceptible to entrainment in the State and Federal water pumps (see

Factor E: Entrainment Losses). In periods with greater freshwater flow into the Delta, X2 is pushed farther downstream (seaward); in periods with low flows, X2 is positioned farther landward (upstream) in the estuary and into the Delta. Not only is longfin smelt abundance in the Bay-Delta strongly correlated with Delta inflow and X2, but the spatial distribution of longfin smelt larvae is also strongly associated with X2 (Dege and Brown 2004, pp. 58-60; Baxter
et al.
2010, p. 61). As longfin hatch into larvae, they move from the areas where they are spawned and

orient themselves just downstream of X2 (Dege and Brown 2004, pp. 58-60). Larval (winter-spring) habitat varies with outflow and with the location of X2 (CDFG 2009, p. 12), and has been reduced since the 1990s due to a general upstream shift in the location of X2 (Hilts 2012, unpublished data). The amount of rearing habitat (salinity between 0.1 and 18 ppt) is also presumed to vary with the location of X2 (Baxter
et al.
2010, p. 64). However, as previously stated, the location of X2 is of particular importance to the distribution of newly-hatched larvae and spawning adults. The influence of water project operations from November through April, when spawning adults and newly-hatched larvae are oriented to X2, is greater in drier years than in wetter years (Knowles 2002, p. 7).

Research on declines of longfin smelt and other pelagic fish species in the Bay-Delta since 2002 (referred to as Pelagic Organism Decline—see Abundance section, above) have most recently been summarized in the Interagency Ecological Program's 2010 Pelagic Organism Decline Work Plan and Synthesis of Results (Baxter
et al.
2010, pp. 61-69). While Baxter
et al.
(2010, pp. 17-19) acknowledge significant uncertainties about the causal mechanisms underlying the Pelagic Organism Decline, they have identified reduced Delta freshwater flows as one of several key factors that they believe contribute to recent declines in the abundance of longfin smelt (Baxter
et al.
2010, pp. 61-69, Figure 5).

Other Populations

Information on effects of reduced freshwater flows on longfin smelt populations other than the Bay-Delta population are lacking. Dams and reservoirs are located in the inland water basins of most of the estuaries where longfin smelt occur. Some of these systems are large and consist of multiple dams and diversions (
e.g.,
Klamath River basin, Columbia River basin). Water diversion systems with dams, canals, and water pipelines located upstream of the estuary may affect longfin smelt aquatic habitat by reducing freshwater flows into the estuary—especially if water is diverted out of the drainage basin—and altering the timing of freshwater flows into the estuary.

Climate Change

“Climate” refers to an area's long-term average weather statistics (typically for at least 20- or 30-year periods), including the mean and variation of surface variables such as temperature, precipitation, and wind, whereas “climate change” refers to a change in the mean and/or variability of climate properties that persists for an extended period (typically decades or longer), whether due to natural processes or human activity (Intergovernmental Panel on Climate Change (IPCC) 2007a, p. 78). Although changes in climate occur continuously over geological time, changes are now occurring at an accelerated rate. For example, at continental, regional, and ocean basin scales, recent observed changes in long-term trends include: a substantial increase in precipitation in eastern parts of North American and South America, northern Europe, and northern and central Asia, and an increase in intense tropical cyclone activity in the North Atlantic since about 1970 (IPCC 2007a, p. 30); and an increase in annual average temperature of more than 2 °F (1.1 °C) across the United States since 1960 (Global Climate Change Impacts in the United States (GCCIUS) 2009, p. 27). Examples of observed changes in the physical environment include: an increase in global average sea level, and declines in mountain glaciers and average snow cover in both the northern and southern hemispheres (IPCC 2007a, p. 30); substantial and accelerating reductions in arctic sea-ice (e.g., Comiso
et al.
2008, p. 1); and a variety of changes in ecosystem processes, the distribution of species, and the timing of seasonal events (
e.g.,
GCCIUS 2009, pp. 79-88).

The IPCC used Atmosphere-Ocean General Circulation Models and various greenhouse gas emissions scenarios to make projections of climate change globally and for broad regions through the 21st century (Meehl
et al.
2007, p. 753; Randall
et al.
2007, pp. 596-599), and reported these projections using a framework for characterizing certainty (Solomon
et al.
2007, pp. 22-23). Examples include: (1) It is virtually certain there will be warmer and more frequent hot days and nights over most of the earth's land areas; (2) it is very likely there will be increased frequency of warm spells and heat waves over most land areas, and the frequency of heavy precipitation events will increase over most areas; and (3) it is likely that increases will occur in the incidence of extreme high sea level (excludes tsunamis), intense tropical cyclone activity, and the area affected by droughts (IPCC 2007b, p. 8, Table SPM.2). More recent analyses using a different global model and comparing other emissions scenarios resulted in similar projections of global temperature change across the different approaches (Prinn
et al.
2011, pp. 527, 529).

All models (not just those involving climate change) have some uncertainty associated with projections due to assumptions used, data available, and features of the models; with regard to climate change this includes factors such as assumptions related to emissions scenarios, internal climate variability, and differences among models. Despite this, however, under all global models and emissions scenarios, the overall projected trajectory of surface air temperature is one of increased warming compared to current conditions (Meehl
et al.
2007, p. 762; Prinn
et al.
2011, p. 527). Climate models, emissions scenarios, and associated assumptions, data, and analytical techniques will continue to be refined, as will interpretations of projections, as more information becomes available. For instance, some changes in conditions are occurring more rapidly than initially projected, such as melting of arctic sea ice (Comiso
et al.
2008, p. 1; Polyak
et al.
2010, p. 1797), and since 2000 the observed emissions of greenhouse gases, which are a key influence on climate change, have been occurring at the mid- to higher levels of the various emissions scenarios developed in the late 1990s and used by the IPPC for making projections (
e.g.,
Raupach
et al.
2007, Figure 1, p. 10289; Manning
et al.
2010, Figure 1, p. 377; Pielke
et al.
2008, entire). Also, the best scientific and commercial data available indicate that average global surface air temperature is increasing and that several climate-related changes are occurring and will continue for many decades even if emissions are stabilized soon (
e.g.
Meehl
et al.
2007, pp. 822-829; Church
et al.
2010, pp. 411-412; Gillett
et al.
2011, entire).

Changes in climate can have a variety of direct and indirect impacts on species, and can exacerbate the effects of other threats. Rather than assessing “climate change” as a single threat in and of itself, we examine the potential consequences to species and their habitats that arise from changes in environmental conditions associated with various aspects of climate change. For example, climate-related changes to habitats, predator-prey relationships, disease and disease vectors, or conditions that exceed the physiological tolerances of a species, occurring individually or in combination, may affect the status of a species. Vulnerability to climate change impacts is a function of sensitivity to those changes, exposure to those changes, and adaptive capacity (IPCC 2007, p. 89;

Glick
et al.
2011, pp. 19-22). As described above, in evaluating the status of a species, the Service uses the best scientific and commercial data available, and this includes consideration of direct and indirect effects of climate change. As is the case with all potential threats, if a species is currently affected or is expected to be affected by one or more climate-related impacts, this does not necessarily mean the species is an endangered or threatened species as defined under the Act. If a species is listed as endangered or threatened, this knowledge regarding its vulnerability to, and impacts from, climate-associated changes in environmental conditions can be used to help devise appropriate strategies for its recovery.

The effects of climate change do not act in isolation, but act in combination with existing threats to species and systems. We considered the potential effects of climate change on the longfin smelt based on projections derived from various modeling scenarios. Temperature increases are likely to lead to a continued rise in sea level, further increasing salinity within longfin smelt estuarine rearing habitat and likely shifting spawning and early rearing upstream as the boundary of fresh and brackish water moves upstream (Baxter 2011, pers. comm.). Reduced snowpack, earlier melting of the snowpack, and increased water temperatures will likely alter freshwater flows, possibly shifting and condensing the timing of longfin smelt spawning (Baxter 2011, pers. comm.).

Effects of climate change could be particularly profound for aquatic ecosystems and include increased water temperatures and altered hydrology, along with changes in the extent, frequency, and magnitude of extreme events such as droughts, floods, and wildfires (Reiman and Isaak 2010, p. 1). Numerous climate models predict changes in precipitation frequency and pattern in the western United States (IPCC 2007b, p. 8). Projections indicate that temperature and precipitation changes will diminish snowpack, changing the availability of natural water supplies (USBR 2011, p. 143). Warming may result in more precipitation falling as rain and less storage as snow. This would result in increased rain-on-snow events and increase winter runoff as spring runoff decreases (USBR 2011, p. 147). Earlier seasonal warming increases the likelihood of rain-on-snow events, which are associated with mid-winter floods. Smaller snowpacks that melt earlier in the year result in increased drought frequency and severity (Rieman and Isaak 2010, p. 6). These changes may lead to increased flood and drought risk during the 21st century (USBR 2011, p. 149).

It is uncertain how a change in the timing and duration of freshwater flows will affect longfin smelt. The melting of the snowpack earlier in the year could result in higher flows in January and February, which are peak spawning and hatching months for longfin smelt. This would reduce adult migration distance and increase areas of freshwater spawning habitat during these months, potentially creating better spawning and larval rearing conditions. Associated higher turbidity may reduce predation on longfin smelt adults and larvae (Baxter 2011, pers. comm.). However, if high flows last only a short period, benefits may be negated by poorer conditions before and after the high flows. As the freshwater boundary moves farther inland into the Delta with increasing sea level (see below) and reduced flows, adults will need to migrate farther into the Delta to spawn, increasing the risk of predation and the potential for entrainment into water export facilities and diversions for both themselves and their progeny.

Global sea level rose at an average rate of 1.8 mm (0.07 in) per year from 1961 to 2003, and at an average rate of 3.1 mm (0.12 in) per year from 1993 to 2003 (IPCC 2007a, p. 49). The IPCC (2007b, p. 13) report estimates that sea levels could rise by 0.18 to 0.58 m (0.6 to 1.9 ft) by 2100; however, Rahmstorf (2007, p. 369) indicated that global sea level rise could increase by over 1.2 m (4 ft) in that time period (CEC 2009, p. 49). Even if emissions could be halted today, the oceans would continue to rise and expand for centuries due to their capacity to store heat (CEC 2009, pp. 49-50). In the Bay-Delta, higher tides combined with more severe drought and flooding events are likely to increase the likelihood of levee failure, possibly resulting in major alterations of the environmental conditions (Moyle 2008, pp. 362-363). It is reasonable to conclude that more severe drought and flooding events will also occur in other estuaries where the longfin smelt occurs. Sea level rise is likely to increase the frequency and range of saltwater intrusion. Salinity within the northern San Francisco Bay is projected to rise 4.5 psu by the end of the century (Cloern
et al.
2011, p. 7). Elevated salinity levels could push the position of X2 farther up the estuary and could result in increased distances that longfin smelt must migrate to reach spawning habitats. Elevated sea levels could result in greater sedimentation, erosion, coastal flooding, and permanent inundation of low-lying natural ecosystems (CDFG 2009, p. 30).

Typically, longfin smelt spawning in the Bay-Delta occurs at water temperatures between 7.0 and 14.5 °C (44.6-58.2 °F), although spawning has been observed at lower temperatures in other areas, such as Lake Washington (Moyle 2002, p. 236). Mean annual water temperatures within the upper Sacramento River portion of the Bay-Delta estuary are expected to approach or exceed 14 °C during the second half of this century (Cloern
et al.
2011, p. 7). Increased water temperatures could compress the late-fall to early-spring spawning period and could result in shorter egg incubation time. Longfin smelt are adapted to hatching in cold, relatively unproductive waters where they grow slowly until ample food resources are available in spring. Warmer water during winter would likely result in increased metabolism of larvae, which may result in increased food needs for maintenance and growth and create a mismatch between food needs and availability (Baxter 2011, pers. comm.). If increased water temperatures compress the spawning period and lead to more synchronized hatching during winter, then prevailing low sunlight and low food resources could result in greater intra-specific (within species) competition (Baxter 2011, pers. comm.). Moreover, increasing water temperatures might also lead to earlier spawning and hatching of other fishes, and to greater inter-specific (between species) competition.

Although climate change and sea level rise are projected to result in continued increases in water temperature and salinity, longfin smelt is considered euryhaline (tolerant of a wide range of salinities) (Moyle 2002, p. 236; Rosenfield and Baxter 2007 p. 1578) and is known to move between different parts of the estuary that vary greatly in temperature and salinity. Being able to move between aquatic habitats that vary greatly in water temperature and salinity may reduce the potential impacts of climate change and sea level rise to some degree.

Channel Disturbances

Dredging and other channel disturbances potentially degrade spawning habitat and cause entrainment loss of individual fish and eggs; disposal of dredge spoils also can create large sediment plumes that expose fish to gill-clogging sediments and possibly to decreased oxygen availability (Levine-Fricke 2004, p. 56). Longfin smelt is a pelagic species (living away from the bottom of the water column and

shoreline), and thus less likely to be directly affected by dredging, sand and gravel mining, and other disturbances to the channel bed compared to bottom-dwelling fish species. Longfin smelt are likely most vulnerable to entrainment by dredging during spawning and egg incubation because eggs are deposited and develop on channel bottom substrates (CDFG 2009, p. 27). Egg development takes approximately 40 days (Moyle 2002, p. 236).

We have found no information documenting population impacts of dredging or sand and gravel mining on longfin smelt. Channel maintenance dredging occurs regularly within the Bay-Delta and other estuaries that serve as shipping channels (e.g., Humboldt Bay, Coos Bay, Yaquina Bay, Columbia River). In their 2009 status review on longfin smelt, CDFG concluded that effects of regular maintenance dredging and sand mining within the Bay-Delta estuary on longfin smelt were expected to be small and localized (CDFG 2009, p. 26). They reviewed two studies on entrainment effects of channel dredging, and each study found that no longfin smelt were entrained during dredging (fish that were entrained were primarily bottom-dwelling species).

There is currently a proposal to deepen and selectively widen the Sacramento Deep Water Ship Channel and the lower portion of the Sacramento River in the Bay-Delta. This dredging project would remove between 6.1-7.6 million cubic meters (8 and 10 million cubic yards) of material from the channel and Sacramento River and extend for 74 km (45.8 mi) (USACE 2011a, entire). Potential effects of this new project to longfin smelt include mortality through loss of spawning substrate, habitat modification, and a shift in spawning and rearing habitat. The project also has potential to alter breeding and foraging behavior of the Bay-Delta longfin smelt population. However, this project is only a proposal at this time and is not certain to occur. Potential effects of the proposed project are currently under evaluation.

Summary of Factor A

Although we find that reduced freshwater flows are currently a threat to the Bay-Delta longfin smelt population, it is difficult to make inferences on the effects of reduced freshwater flows to longfin smelt populations throughout the species range. Because the Bay-Delta system includes one of the largest man made water system in the world, it would be impractical to compare diversions and alterations in other estuaries to diversions and alterations in the Bay-Delta. The effects of water development in the Bay-Delta are unique to the physical, geologic, and hydrologic environment of the estuary. Reduced flow from diversions and dams in other estuaries is not expected to be as significant as the reduced flows that have been shown in the Bay-Delta because less water is exported from other estuaries. We have no information to show that reduced freshwater flow is a threat to longfin smelt in other estuaries. Therefore, we conclude that while reduced flow is a threat to the Bay-Delta population of longfin smelt, the best available science does not indicate that the lack of freshwater flow is a threat to the species in other parts of its range.

Climate change will likely affect longfin smelt in multiple ways, but longfin smelt are able to move between a wide range of aquatic environments that vary greatly in water temperature and salinity. These behavioral and physiological characteristics of the species may help it adapt to effects of climate change. We conclude at this time that the best available information does not indicate that climate change threatens the continued existence of longfin smelt across its range.

Channel disturbances may have localized impacts to longfin smelt habitat suitability, but the best available information does not indicate that they pose significant threats to the species throughout its range.

Based on the best available scientific information, we conclude that reduced freshwater flows, climate change, and channel disturbances are not significant current or future threats to longfin smelt across its range except in the Bay-Delta, where reduced freshwater flow is a threat.

Factor B. Overutilization for Commercial, Recreational, Scientific, or Educational Purposes

Recreational and Commercial Fishing

In California, longfin smelt was listed as a threatened species under the State's Endangered Species Act in 2009. This status makes take of longfin smelt illegal, unless authorized by an incidental take permit or other take authorization. However, longfin smelt are caught as bycatch in small bay shrimp trawl fishery and bait fishing (anchovies and sardines) operations in South San Francisco Bay, San Pablo Bay, and Carquinez Strait (CDFG 2009a, p. 1). CDFG (2009d, pp. 6, 9) estimated the total longfin smelt bycatch from shrimping in 1989 and 1990 at 15,539 fish, and in 2004 at 18,815-30,574 fish. CDFG noted in 2009 that the bay shrimp trawl fishery industry had declined since 2004 (CDFG 2009d, p. 3). No shrimp fishery currently takes place in Humboldt Bay (Mello 2011, pers. comm.).

In Oregon, smelt species may not be targeted in commercial fisheries, and if taken incidentally, smelt catch cannot exceed 1 percent of the total weight landed (ODFW 2011, p. 17). Rules limit in which estuaries bait fishing for herring, sardines, anchovies, and shad may occur. In Oregon, there is currently no known shrimping taking place within the estuaries where the longfin smelt might be found. Although a limited entry roe herring fishery is allowed in Yaquina Bay, no landings have occurred there since 2003, because biomass estimates have generally been too low to make the fishery economically viable (Krutzikowsky 2011, pers. comm.). Anchovy fishing is allowed in Tillamook Bay, Yaquina Bay, and Coos Bay, but because there is currently no anchovy fishing occurring in these areas (Krutzikowsky 2011, pers. comm.), longfin smelt are not taken as bycatch. Records for commercial landings in Oregon show a total of 9.1 kilograms (kg) (20 pounds (lb)) landed from 2005 to 2010 for smelt species other than eulachon. Recreational fishing for smelt species is allowed only in marine waters (Oregon Sport Fishing Regulations, p. 11).

The State of Washington includes longfin smelt in a class of fish referred to as forage fish (small schooling fish that are major food items for many species of fish, birds, and marine mammals) (Bargmann 1998, p. 1). Both recreational and commercial fisheries exist for forage fish in Washington, but the recreational fishery is much smaller than the commercial fishery. A sport fishing license is not needed to catch smelt. Smelt can be harvested recreationally using a dip net or jig. Dip net fishing for longfin smelt is allowed in the Nooksack River and there are approximately two hundred trips a year made to fish for longfin smelt in this area (O'Toole 2011, pers. comm.). It is unlawful to use a herring or smelt rake. Sport and tribal commercial fisheries have been reported to occur on the Nooksack River longfin smelt stock (Bargmann 1998, p. 37). Longfin smelt may be caught incidentally in a medium-sized shore or pier-based recreational fishery for surf smelt in Puget Sound.

There is currently no commercial fishing regulation specific to longfin smelt in Washington (Paulson 2011, pers. comm.). The daily limit for smelt is 4.5 kg (10 lb) and, like Oregon, is counted as an aggregate, which can include herring, sardines, sandlance,

and anchovies (WDFW 2011, p. 27). There is a robust commercial herring fishery in Washington that takes approximately 450 metric tons (500 tons) of fish per year (for sport bait) and a commercial surf smelt fishery that takes approximately 450,000 kg (100,000 lb) of fish per year (for human consumption). Longfin smelt bycatch in both of these fisheries is low. Anchovy fishing in Washington primarily takes place in Grays Harbor and the mouth of the Columbia River (O'Toole 2011, pers. comm.).

In British Columbia, take of smelt from recreational fishing is limited to 20 kilograms (kg) (44 lb) per day and 40 kg (88 lb) of total catch in possession. The fishing season takes place from April 1 to June 14 (Department of Fisheries and Oceans Canada 2011a, p. 47). A commercial fishing industry targeting surf smelt may incidentally take longfin smelt (Department of Fisheries and Oceans Canada 2011b, p. 1). British Columbia supports a year-round shrimp fishery in Prince Rupert and Chatham Sound. Sardine and shrimp fishing occurs near Vancouver.

In Alaska, a commercial fishery for smelt, which includes eulachon, was reopened in 2005. This fishery is restricted to the brackish waters of Cook Inlet, from May 1 to June 30. The total annual harvest of eulachon and longfin smelt may not exceed 90 metric tons (100 tons) of smelt. However, longfin smelt are unlikely to be specifically targeted in this fishery due to their small numbers in relation to eulachon in the region (Shields 2005, p. 4). Sport fishing is limited to salt water, where herring and smelt may be taken (Alaska Department of Fish and Game (ADFG) 2010, p. 1). In Prince William Sound, the herring fishery has closed due to low abundance of herring.

Monitoring Surveys

Fisheries monitoring surveys are conducted by NOAA's National Marine Fisheries Service, the Service and by State and local agencies in water bodies inhabited by longfin smelt throughout their range. Most of these surveys target other species, primarily salmonids, and rarely collect longfin smelt outside of the Bay-Delta area.

Within the Bay-Delta, longfin smelt are regularly captured in monitoring surveys. The Interagency Ecological Program (IEP) implements scientific research in the Bay-Delta. Although the focus of its studies and the level of effort have changed over time, in general, their surveys have been directed at researching the Pelagic Organism Decline in the Bay-Delta. Between the years of 1987 to 2011, combined take of longfin smelt less than 20 mm (0.8 in) in length ranged from 2,405 to 158,588 annually. All of these fish were preserved for research or assumed to die in processing. During the same time period, combined take for juveniles and adults (fish greater than or equal to 20 mm (0.8 in)) ranged from 461 to 68,974 annually (IEP 2011, no pagination). Although mortality is unknown, the majority of these fish likely do not survive. The Chipps Island survey, which is conducted by the Service, has captured an average of 2,697 longfin smelt per year during the past 10 years. Biologists attempt to release these fish unharmed, but at least 5,154 longfin smelt were known to have died during the Chipps Island survey between 2001 and 2008 (Service 2010, entire).

Survey methods have been modified recently to minimize potential impacts to delta smelt, a related species that also occurs in the Bay-Delta (75 FR 17669; April 7, 2010). These modifications are likely to result in reduced impacts to longfin smelt also. The Service conducts other surveys in the Bay-Delta to monitor salmon populations (Mossdale trawl, Sacramento trawl, beach seine surveys), but few longfin smelt are captured during these surveys. Mortality due to monitoring surveys was not identified by the Interagency Ecological Program in its most recent synthesis of results as a factor in the decline of longfin smelt and other pelagic fish species in the Bay-Delta since the early 2000s (Baxter
et al.
2010, pp. 19-53, 61-69).

Summary of Factor B

The species is incidentally caught in commercial shrimp and bait fishing operations throughout much of its range, but the bycatch numbers are usually low. In California, take of longfin smelt is illegal without authorization because the species is listed as threatened under the California Endangered Species Act. Because of its small size, it is not targeted by recreational angling, although it is certainly caught and used as bait for other larger recreational fish species. Monitoring surveys have resulted in high numbers of longfin smelt mortality in the Bay-Delta in the past, but efforts being made to reduce survey mortality for delta smelt, such as reductions in tow times, likely have also benefitted longfin smelt. The scientific collection surveys being conducted in the Bay-Delta are limited to research designed to benefit the species, and mortality from monitoring surveys has not been identified as a factor in the longfin smelt's recent population decline. We have no information indicating that mortality from monitoring surveys threatens any populations within the species' range. We conclude that overutilization due to commercial, recreational, or scientific take is not a significant current or future threat to the longfin smelt throughout its range.

Factor C. Disease or Predation

Disease

All the information we found on disease in longfin populations originated from studies in the Bay-Delta. Two investigations published in 2006 and 2008 by the California-Nevada Fish Health Center detected no significant health problems in juvenile longfin smelt in the Bay-Delta (Foott and Stone 2008, pp. 15-16). The low observed rate of parasitic infection did not appear to affect the health of the fish, as indicated by the lack of associated tissue damage or inflammation (Foott and Stone 2008, p. 15). The only additional documentation of relevant wild fish disease in the Bay-Delta was a severe intestinal infection by a new species of myxozoan observed in nonnative juvenile yellowfin goby (
Acanthogobius flavimanus
) from Suisun Marsh (Baxa
et al.
in prep cited in

Baxter
et al.
2008, p. 16). The nonnative gobies could act as potential vectors of the parasite to other susceptible species in the Bay-Delta. It is unknown whether this or similar infections are affecting the health of longfin smelt.

The south Delta is fed by water from the San Joaquin River, where pesticides (
e.g.,
chlorpyrifos, carbofuran, and diazinon), salts (e.g., sodium sulfates), trace elements (boron and selenium), and high levels of total dissolved solids are prevalent due to agricultural runoff (64 FR 5963; February 8, 1999). Pesticides and other toxic chemicals may adversely affect the immune system of longfin smelt and other fish in the Bay-Delta and other estuaries, but we found no information documenting such effects (see Factor E: Contaminants, below).

Predation

As a forage species, longfin smelt are preyed upon by a variety of fishes, birds, and mammals (Barnhart
et al.
1992, p. 44). However, we found little information on predation of longfin smelt other than information for the Bay-Delta population and Lake Washington population. The striped bass (
Morone saxatilis
) is a potential predator of longfin smelt in the Bay-Delta. Striped bass were introduced into the Bay-Delta in 1879 and quickly became abundant throughout the estuary. However, their numbers have

declined substantially over the last 40 years (Thomson
et al.
2010, p. 1440), and they are one of the four species studied under Pelagic Organism Decline investigations (Baxter
et al.
2010, p. 16). Numbers of largemouth bass (
Micropterus dolomieui
), another introduced species in the Bay-Delta, have increased in the Delta over the past few decades (Brown and Michniuk 2007, p. 196). Largemouth bass, however, occur in shallow freshwater habitats, closer to shore than the pelagic longfin smelt, and do not typically co-occur with longfin smelt. Baxter
et al.
(2010, p. 40) reported that no longfin smelt have been found in largemouth bass stomachs sampled in a recent study of largemouth bass diet. Moyle (2002, p. 238) believed that inland silverside (
Menidia beryllina
), another nonnative predatory fish, may be an important predator on longfin smelt eggs, larvae, juveniles, and adults. Rosenfield (2010, p. 18) acknowledged that they are likely major predators of longfin smelt eggs and larvae but thought it unlikely that they were an important predator on juveniles and subadults because inland silversides prefer shallow water habitats whereas juvenile and subadult longfin smelt do not.

In the Bay-Delta, predation of longfin smelt may be high in the Clifton Court Forebay, where the SWP water export pumping plant is located (Moyle 2002, p. 238; Baxter
et al.
2010, p. 42). However, once they are entrained in the Clifton Court Forebay, longfin smelt mortality would be high anyway due to high water temperatures in the forebay (CDFG 2009b, p. 4) and entrainment into the SWP water export pumping plant. In addition to elevated predation levels in the Clifton Court Forebay, predation also is concentrated at sites where fish salvaged from the SWP and CVP export facilities are released (Moyle 2002, p. 238). However, few longfin smelt survive the salvage and transport process (see Factor E: Entrainment Losses, below) and therefore predation is not expected to be an important factor at drop-off sites. Reduced freshwater flows may result in lower turbidity and increased water clarity (see Factor A, above), which may contribute to increased risk of predation (Baxter
et al.
2010, p. 64).

In Lake Washington, longfin are preyed upon by prickly sculpin (
Cottus asper
) (Tabor
et al.
2007, p. 1085) and cutthroat trout (
Oncorhynchus clarki
) (Norwak
et al.
2004, p. 632; Beauchamp
et al.
1992, p. 156). Cutthroat trout have displaced the northern pikeminnow as the most important predator in Lake Washington and may be having an effect on other components of the ecosystem, including longfin smelt populations (Norwak
et al.
2004, pp. 633-634).

Summary of Factor C

Similar to other threats, very little information is available about disease or predation threats to longfin smelt populations outside of the Bay-Delta. We found no information that disease is a threat to the longfin smelt throughout its range. Longfin smelt is a small fish that is preyed upon by a wide variety of fish, birds, and mammals, but we found no information documenting predation as a threat to the species rangewide. Predation, along with mortality from entrainment (see Factor E: Entrainment Losses, below), has been identified as a top-down effect that may be contributing to recent declines of longfin smelt and other pelagic fish species in the Bay-Delta estuary (Pelagic Organism Decline) (Sommer
et al.
2007, p. 275). However, factors contributing to the Pelagic Organism Decline are numerous and complex, and the combination of underlying causal mechanisms remains uncertain (Baxter
et al.
2010, pp. 61-69). Therefore, based on our review of the best available scientific and commercial information, we conclude that disease or predation are not significant current or future threats to the longfin smelt throughout its range.

Factor D. The Inadequacy of Existing Regulatory Mechanisms

Federal Laws

A number of federal environmental laws and regulations exist that may provide some protection for longfin smelt: the National Environmental Policy Act, the Central Valley Project Improvement Act, and the Clean Water Act.

National Environmental Policy Act

The National Environmental Policy Act (NEPA) (42 U.S.C. 4321
et seq.
) requires all Federal agencies to formally document, consider, and publicly disclose the environmental impacts of major Federal actions and management decisions significantly affecting the human environment. NEPA documentation is provided in an environmental impact statement, an environmental assessment, or a categorical exclusion, and may be subject to administrative or judicial appeal. However, the Federal agency is not required to select an alternative having the least significant environmental impacts, and may select an action that will adversely affect sensitive species provided that these effects are known and identified in a NEPA document. Therefore, we do not consider the NEPA process in itself is to be a regulatory mechanism that is certain to provide significant protection for the longfin smelt.

Central Valley Project Improvement Act

The Central Valley Project Improvement Act (Pub. L. 102-575) (CVPIA) amends the previous Central Valley Project authorizations to include fish and wildlife protection, restoration, and mitigation as project purposes having equal priority with irrigation and domestic uses, and fish and wildlife enhancement as having an equal priority with power generation (Pub. L. 102-575, October 30, 1992; Bureau of Reclamation 2009). Included in CVPIA section 3406 (b)(2) was a provision to dedicate 800,000 acre-feet of Central Valley Project yield annually (referred to as “(b)(2) water”) for fish, wildlife, and habitat restoration. Since 1993, (b)(2) water has been used and supplemented with acquired environmental water (Environmental Water Account and CVPIA section 3406 (b)(3) water) to increase stream flows and reduce Central Valley Project export pumping in the Delta. These management actions were taken to contribute to the CVPIA salmonid population doubling goals and to protect Delta smelt and their habitat (Guinee 2011, pers. comm.). As discussed above, (see Biology and Factor A discussions), increased freshwater flows have been shown to be positively correlated with longfin smelt abundance; therefore, these management actions, although targeted towards other species, should also benefit longfin smelt.

Clean Water Act

Established in 1977, the Clean Water Act (33 U.S.C. 1251
et seq.
) is the primary Federal law in the United States regulating water pollution. It employs a variety of regulatory and non-regulatory means to reduce direct water quality impacts and manage polluted runoff. The Clean Water Act provides the basis for the National Pollutant Discharge Elimination System (NPDES) and gives the Environmental Protection Agency (EPA) the authority to set effluent limits and require any entity discharging pollutants to obtain a NPDES permit. The EPA is authorized through the Clean Water Act to delegate the authority to issue NPDES permits to State governments and has done so in California. In States that have been authorized to implement Clean Water Act programs, EPA retains oversight responsibilities. Water bodies that do not meet applicable water quality

standards are placed on the section 303(d) list of impaired water bodies, and the State is required to develop appropriate total maximum daily loads (TMDL) for the water body. A TMDL is a calculation of the maximum amount of a pollutant that a water body can receive and still meet water quality standards. At present, TMDLs are not in place in all impaired watersheds in which longfin smelt are known to occur. The Clean Water Act has not effectively limited ammonia input into the system, and ammonia has been shown to negatively affect the longfin smelt's food supply.

State Laws

The State of California has a number of environmental laws and regulations which may provide some protection for longfin smelt: California Endangered Species Act, California Environmental Quality Act, California Marine Invasive Species Act, Porter-Cologne Water Quality Control Act, and regulatory prohibitions on streambed alterations.

California Endangered Species Act

Longfin smelt was listed as threatened under the California Endangered Species Act (CESA) (California Fish and Game Code 2050
et seq.
) in 2009. The CESA prohibits unpermitted possession, purchase, sale, or take of listed species. However, the CESA definition of take does not include harm, which under the Act's implementing regulations includes significant modification or degradation of habitat that actually kills or injures wildlife by significantly impairing essential behavioral patterns (50 CFR 17.3). CESA allows take of species for otherwise lawful projects through use of an incidental take permit. An incidental take permit requires that impacts be minimized and fully mitigated (CESA sections 2081 (b) and (c)). Furthermore, CESA requires that the issuance of the permit will not jeopardize the continued existence of a State-listed species. The CESA does require consultation between CDFG and other State agencies to ensure that activities of State agencies will not jeopardize the continued existence of State-listed species (CERES 2009, p. 1). Longfin Smelt Incidental Take Permit No. 2081-2009-001-03 specifies that the Smelt Working Group, which was created under the Service's 2008 delta smelt biological opinion (Service 2008, p. 30), provide recommendations for export pumping reduction to CDFG if any of several criteria is reached. One of the criteria is that total salvage of adult longfin smelt (fish greater than or equal to 80 mm in length) at the State Water Project and Central Valley Project export pumps between December and February may not exceed five times the Fall Midwater Trawl longfin smelt annual abundance index. Also, if longfin abundance is low and surveys indicate that adults are distributed close to the export pumps, the Smelt Working Group may consider making recommendations for Old and Middle River Flows that would reduce pumping (CDFG 2009c, pp. 1-34; Smelt Working Group 2011, p. 4).

California Environmental Quality Act

The California Environmental Quality Act ((CEQA) (Public Resources Code section 21000
et seq.
)) requires review of any project that is undertaken, funded, or permitted by the State of California or a local government agency. If significant effects are identified, the lead agency has the option of requiring mitigation through changes in the project or to decide that overriding considerations make mitigation infeasible (CEQA sec. 21002). In the latter case, projects may be approved that cause significant environmental damage, such as destruction of listed endangered species or their habitat. Protection of listed species through CEQA is, therefore, dependent on the discretion of the lead agency. The CEQA review process ensures that a full environmental review is undertaken prior to the permitting of any project within longfin smelt habitat.

California Marine Invasive Species Act

The California Marine Invasive Species Act (AB 433) was passed in 2003. This 2003 act requires ballast water management for all vessels that intend to discharge ballast water in California waters. All qualifying vessels coming from ports within the Pacific Coast region must conduct an exchange in waters at least 50 nautical mi offshore and 200 m (656 ft) deep or retain all ballast water and associated sediments. To determine the effectiveness of the management provisions of this 2003 act, the legislation also requires State agencies to conduct a series of biological surveys to monitor new introductions to coastal and estuarine waters. These measures should further minimize the introduction of new invasive species into California's coastal waters that could be a threat to the longfin smelt. The Coastal Ecosystems Protection Act of 2006 deleted a sunset provision of the Marine Invasive Species Act, making the program permanent.

Porter-Cologne Water Quality Control Act

The Porter-Cologne Water Quality Control Act (California Water Code 13000
et seq.
) is a California State law that establishes the State Water Resources Control Board (SWRCB) and nine Regional Water Quality Control Boards that are responsible for the regulation of activities and factors that could degrade California water quality and for the allocation of surface water rights (California Water Code Division 7). In 1995, the SWRCB developed the Bay-Delta Water Quality Control Plan that established water quality objectives for the Delta. This plan is currently implemented by Water Rights Decision 1641, which imposes flow and water quality standards on State and Federal water export facilities to assure protection of beneficial uses in the Delta (USFWS 2008, pp. 21-27). The various flow objectives and export restraints were designed, in part, to protect fisheries. These objectives include specific freshwater flow requirements throughout the year, specific water export restraints in the spring, and water export limits based on a percentage of estuary inflow throughout the year. The water quality objectives were designed to protect agricultural, municipal, industrial, and fishery uses; they vary throughout the year and by the wetness of the year.

In December 2010, the California Central Valley Regional Water Quality Control Board (Regional Board) adopted a new National Pollutant Discharge and Elimination System (NPDES) permit for the Sacramento Regional Wastewater Treatment Plant to address ammonia loading to the Sacramento River and the Delta. In January 2011, the Sacramento Regional County Sanitation District petitioned the Regional Board for a review of the permit, which may require a year or more. There is currently no TMDL in place for ammonia discharge into the Sacramento watershed. The EPA is currently updating freshwater ammonia criteria that will include new discharge limits on ammonia (EPA 2009, pp. 1-46). Ammonia has been shown to have negative effects on prey items that longfin smelt rely upon (see Factor E: Contaminants, below). This regulation does not adequately mitigate potential negative effects to longfin smelt from ammonia in the Bay-Delta.

Streambed Alteration

In California, section 1600
et seq.
of the California Fish and Game Code authorizes CDFG to regulate streambed alteration. The CDFG must be notified of and approve any work that substantially diverts, alters, or obstructs the natural flow or that substantially changes the bed, channel, or banks of any river, stream, or lake. If an existing fish or wildlife resource, including longfin smelt, may be substantially adversely

affected by a project, the project proponent must submit proposals to protect the species to the CDFG at least 90 days before the start of the project. However, these proposals are subject to agreement by the project proponent. If CDFG deems proposed measures to be inadequate, a third party arbitration may be initiated. However, projects that cause significant environmental damage such as destruction of species and their habitat including longfin smelt may be approved because the CDFG has no authority to deny requests for streambed alteration.

Oregon Environmental Regulations

Oregon classifies longfin smelt as a native migratory fish under Oregon Administrative Rule (Division 412, 635-412-0005). Operators of artificial obstructions located in waters in which any native migratory fish are currently or were historically present must provide for fish passage requirements during installation, replacement, or abandonment of artificial obstructions (ODFW 2011, p. 1). This State law helps ensure passage of migratory longfin smelt between rearing and spawning habitat.

Washington Environmental Regulations

Washington's State Environmental Policy Act (RCW 43.21C) provides a process similar to CEQA and is applicable to every State and local agency in Washington State. This law requires State and local governments to consider impacts to the environment and include public participation in project planning and decision making (Washington Division of Wildlife 2011, p. 1). Project proponents must submit a proposal for their project to the appropriate city, county, or State lead agency where the project is taking place. The lead agency then makes a determination of whether or not the project will have significantly adverse environmental impacts. The lead agency then may require the applicant to change the proposal to minimize environmental impacts or in rare cases may deny the application (Washington State Department of Ecology (WSDE) 2002, pp. 1-2).

Alaska Environmental Regulations

The Anadromous Fish Act (AS 16.05.871-.901) requires that anyone desiring to alter a streambed or waterbody first obtain a permit from the Alaska Department of Fish and Game (ADFG). Regulated activities include construction, road crossings, gravel mining, water withdrawal, stream realignment, and bank stabilization. Although there are no minimization or mitigation components to this law, the ADFG commissioner has the ability to deny a permit if he or she finds the plans and specifications are insufficient for the proper protection of anadromous fish. The Fishway or Fish Passage Act (AS 15.05.841) requires that activities within or crossing a stream obtain permission from ADFG if they will impede the passage of resident or anadromous fish. This provides some degree of protection for longfin smelt, which is categorized as an anadromous fish in the State of Alaska.

Canadian Environmental Regulations

The Canadian Environmental Assessment Act (S.C. 1992, c. 37) was passed by the Canadian Parliament in 1992. The Act requires Federal departments to conduct environmental assessments for proposals where the government is the proposer or the project involves Federal funding or permitting. The Canadian Environmental Protection Act of 1999 is intended to prevent pollution, protect the environment and human health, and contribute to promoting sustainable development. Canada has the Canadian Environmental Protection Act (CEPA), which is equivalent to the United States' NEPA. It was enacted to protect Canada's natural resources through pollution prevention and sustainable development. This provides some level of protection for longfin smelt from pollution and habitat degradation. The longfin smelt is not currently a protected species under the Species at Risk Act (SARA) of 2002 (S.C. 2002 c. 29; SARA). SARA is similar to the United States' Endangered Species Act. If the longfin smelt were determined by the Canadian government to need protection in the future, it could be listed under SARA.

Summary of Factor D

We evaluate existing regulatory mechanisms that have an effect on threats that we have identified elsewhere in the threats analysis. We do not evaluate the lack of a regulatory mechanism that may address a particular threat if that regulatory mechanism does not exist. We find that the threats to the longfin smelt and its habitat on Federal, State, and private lands on a range-wide basis are minimal (Factors A, B, C and E). Existing federal regulatory mechanisms provide a degree of protection for longfin smelt from these threats. Therefore, we find that regulatory mechanisms provide adequate protections to longfin smelt and its habitat throughout its range.

Factor E. Other Natural or Manmade Factors Affecting Its Continued Existence

Other natural or manmade factors potentially affecting the continued existence of longfin smelt include entrainment losses from water diversions, introduced species, and contaminants.

Entrainment Losses

The only information we found on entrainment losses of longfin smelt comes from the Bay-Delta population. Entrainment occurs when fish are drawn toward water diversions, where they are typically trapped or killed. In the Bay-Delta, water is diverted and fish potentially entrained at four major water export facilities within the Delta, two power plants, and numerous small water diversions throughout the Delta for agriculture and in Suisun Marsh for waterfowl habitat. In their 2009 status review of longfin smelt, CDFG (2009, pp. 19-26) summarized entrainment losses at these water diversions.

Water Export Facilities

The four State and Federal water export facilities (pumping stations) in the Delta are the State Water Project (SWP) facility in the south Delta, the Central Valley Project (CVP) in the south Delta, the Contra Costa facility in the south Delta, and the North Bay Aqueduct facility in the north Delta. The SWP and CVP facilities pump the majority of the water exported from the Delta. Average annual volumes of water exported from these facilities between 1995 and 2005 were 3.60 km
3
at the SWP facility, 3.10 km
3
at the CVP facility, 0.15 km
3
at the Contra Costa facility, and 0.05 km
3
at the North Bay Aqueduct facility (Sommer
et al.
2007, p. 272). Depending on upstream flow through the Delta, operation of the SWP and CVP facilities often causes reverse flows in the river channels leading to them; longfin smelt that occupy these channels during certain times of the year may be entrained by these reverse flows. The SWP and CVP water export facilities are equipped with their own fish collection facilities that divert entrained fish into holding pens using louver-bypass systems to protect them from being killed in the pumps. The fish collected at the facilities are referred to as “salvaged,” and are loaded onto tanker trucks and returned to the western Delta downstream (Aasen 2009, p. 36). The movement of fish can result in mortality due to overcrowding in the tanks, stress, moving procedures, or predation at locations where the fish are released. Salvage is an
index
of

entrainment, not an estimate, and is much smaller than total entrainment (Castillo
et al.
in review). Of spawning age fish (age-1 and age-2), which contribute most to longfin smelt population dynamics in the Bay-Delta, the total number of longfin smelt salvaged at both pumps between 1993 and 2007 was 1,133 (CDFG 2009, Attachment 3, p. 2).

Fish entering the intake channel of the CVP or the radial gates of the 31,000-acre Clifton Court Forebay reservoir (SWP) are considered entrained (Fujimura 2009, p. 5; CDFG 2009b, p. 2). Most longfin smelt that become entrained in Clifton Court Forebay are unable to escape (CDFG 2009b, p. 4). The number of fish entrained at the SWP and CVP facilities has never been determined directly, but entrainment losses have been estimated indirectly using data from research and monitoring efforts. The magnitude of entrainment of larval longfin smelt is unknown because only fish greater than 20 mm in length are salvaged at the two facilities (Baxter
et al.
2008, p. 21). In years with low freshwater flows, approximately half of the longfin smelt larvae and early juveniles may remain for weeks within the Sacramento-San Joaquin Delta (Dege and Brown 2004), where model simulations indicate they are vulnerable to entrainment into State Water Project, Central Valley Project, and other diversions (Kimmerer and Nobriga 2008, CDFG 2009a, p. 8).

Entrainment is no longer considered a major threat to longfin smelt in the Bay-Delta because of current regulations. Efforts to reduce delta smelt entrainment loss through the implementation of the 2008 delta smelt biological opinion and the listing of longfin smelt under the CESA have likely reduced longfin smelt entrainment losses. The high rate of entrainment that occurred in 2002 that threatened the Bay Delta longfin smelt population is unlikely to recur, and would no longer be allowed under today's regulations because limits on longfin smelt take due to CESA regulations (see Factor D discussion, below) would trigger reductions in the magnitude of reverse flows.

Power Plants

Two power plants located near the confluence of the Sacramento and San Joaquin Rivers, the Contra Costa Generating Station and the Pittsburg Generating Station, pose an entrainment risk to longfin smelt. Past entrainment losses of delta smelt at these two facilities were significant and considered a threat to delta smelt (75 FR 17671; April 7, 2010). Power plant operations have been substantially reduced since the late 1970s, when high entrainment and impingement were documented (CDFG 2009, p. 24); the power plants are now either kept offline or operating at very low levels, except as necessary to meet peak power needs. From 2007-2010, capacity utilization of these units averaged only 2.3 percent of maximum capacity. No longfin smelt were detected during impingement sampling conducted between May of 2010 and April of 2011 to monitor entrainment losses at the two power plants (Tenera Environmental 2011, entire). The company that owns the two power plants has committed to retiring one of the two power stations in 2013 (Contra Costa Generating Station) and has made this commitment enforceable through amendments to its Clean Air Act Title V permit (Raifsnider 2011, pers. comm.).

Agricultural Diversions

Water is diverted at numerous sites throughout the Bay-Delta for agricultural irrigation. Herren and Kawasaki (2001) reported over 2,200 such water diversions within the Delta, but CDFG (2009, p. 25) notes that number may be high because Herren and Kawasaki (2001) did not accurately distinguish intake siphons and pumps from discharge pipes. CALFED's Ecosystem Restoration Program (ERP) includes a program to screen remaining unscreened small agricultural diversions in the Delta and the Sacramento and San Joaquin Rivers. The purpose of screening fish diversions is to prevent entrainment losses; however, very little information is available on the efficacy of screening these diversions (Moyle and Israel 2005, p. 20). Agricultural operations begin to divert water in March and April, and many longfin smelt have begun leaving the Delta by this time. Water diversions are primarily located on the edge of channels and along river banks. Longfin smelt are a pelagic fish species and tend to occupy the middle of the channel and the middle of the water column, where they are unlikely to be vulnerable to entrainment into these diversions.

Suisun Marsh Diversions

There are 366 diversions in Suisun Marsh used to enhance waterfowl habitat (USFWS 2008, p. 172). Water is pumped at these diversions between October and May. Longfin larvae are abundant in the Marsh from February through April, while adults are abundant from October to February (Meng and Mattern 2001, p. 756; Rosenfield and Baxter 2007, p. 1588). During a 2-year study sampling 2.3 million m
3
(81.2 million ft
3
) of water entering intakes, entrainment was found to be low, capturing only 124 adult longfin and 160 larvae (Enos
et al.
2007, p. 16). Restrictions on pumping have been put in place to protect delta smelt and salmon. These restrictions likely also benefit longfin smelt.

Introduced Species

Nonnative introduced species (both plants and animals) are common in many of the estuaries within the range of the longfin smelt. Introduced species can significantly alter food webs in aquatic

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Source: Frix Law Library, https://www.frixlaw.com/law-library/documents/fr%3A2012-7198. Public record. Not legal advice.