	1898	1934	1940-41	1970-71
Native Species
Pacific lamprey	Probably	Probably	Probably	Yes
Pacific brook lamprey	Probably	Probably	Probably	Yes
Rainbow trout	Yes	Yes	Yes	Yes
Chinook salmon	Yes	Yes	Yes	No
Sacramento blackfish	Probably	Yes	Yes	No
Hitch	Yes	Yes	Yes	No
Hardhead	Yes	Yes	Yes	No
Splittail	Yes	No	No	No
California roach	Yes	Yes	Yes	No
Sacramento squawfish	Yes	Yes	Yes	No
Sacramento sucker	Yes	Yes	Yes	Yes
Tule perch	Yes	Yes	Yes	No
Prickly sculpin	Yes	Yes	Yes	Yes
Threespine stickleback	Yes	Yes	Yes	Yes

Introduced Species
Brown trout	No	Yes	Yes	Yes
Carp	No	Yes	Yes	Yes
Brown bullhead	No	No	Yes	Yes
Mosquitofish	No	No	Yes	Yes
Green sunfish	No	No	Yes	Yes
Bluegill	No	Yes	Yes	Yes
Smallmouth bass	No	Yes	Yes	No
Largemouth bass	No	No	Yes	Yes

Total Species	14	17	21	13

Percent Native Species	100	77	62	40

The community of native fishes that once dominated the lakes, sloughs, and rivers of the Valley floor has been largely replaced by nonnative sunfishes, catfishes, and carp (see Table ) (Moyle 1976). These introduced species have proven more successful in disturbed and artificially-created freshwater habitats than the native species. At least two native species are no longer found in their original habitat: the thicktail chub is believed to be extinct, and the Sacramento perch is restricted to some farm ponds (Moore et al. 1990).

Relatively little information is available about the historical fishery of the large lakes of the Tulare Basin, as they were apparently drained before for farmland before their fish fauna was surveyed (Moyle 1976). However, the lakes were probably important habitat for Sacramento perch, the presumably-extinct thicktail chub, and other native fishes (Moyle 1976).

Conditions in the San Joaquin River, which remains the most valuable fish habitat in the Valley, are detailed in a July 11, 1991, letter from the California Department of Fish and Game. This letter, which also discusses potential mitigation measures along the river, is included as Attachment A. Appendix 3 provides a list of common native and introduced fish species found in the San Joaquin River downstream of Friant Dam.

Fisheries

Fisheries resources within the San Joaquin Valley are affected by water availability and adjacent land uses. In the upper San Joaquin River and tributary streams, snow-fed perennial flows sustain both cold water and warm water fish. Historically, the native fish fauna of the San Joaquin Valley included true freshwater fishes, anadromous fishes, and, in the San Francisco Bay-San Joaquin Delta, fishes of marine origin (Moyle 1976). Today, introduced species, such as striped bass, American shad, largemouth bass, and catfishes, generally out-compete native species in habitats altered by the influences of drainwater, reservoirs, and water diversions. Native fishes have been reduced to a minor part of the fauna. Native freshwater fishes can now be found only in relatively undisturbed reaches of the San Joaquin Valley. The spring run of chinook salmon is now extinct in the San Joaquin drainage, and the fall run now occurs in much reduced and dramatically low numbers in major tributaries to the San Joaquin River as shown in Table , the Merced, Tuolumne, Consumnes, Stanislaus, and Mokelumne rivers (CDFG 1992). W.E. Loudermilk, California Department of Fish and Game, stated that the 1991 salmon count for the Merced River stood at 58 returning salmon, of these salmon most returned to the Merced hatchery, but a few natural spawners remained in the River (exact number of remaining natural spawners was unavailable, personal communication, Loudermilk, June 26, 1992).

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Table . Comparison of recent San Joaquin River Basin chinook salmon escapements to historic high escapement levels (from CDFG 1992).

ÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄ

Year Stanislaus Tuolumne Merced San Joaquin Total

1983 500 14,800 18,200 0^a 33,500

1984 12,000 14,000 23,000 0 49,000

1985 13,000 41,000 16,000 0 70,000

1986 6,000 7,00 5,000 0 18,000

1987 6,400 14,900 3,900 0 25,200

1988 12,300 6,300 3,200 2,300^b 24,100

1989 1,543 1,274 211 322^b 3,028

1990 492 96 73 280^b 941

Historic 35,000 22,000 23,000 6,000 na

high (1953) (1940) (1984) (1945)

^{a. Friant Dam closed in 1945, with inadequate

stream flow requirements.}

^{b. Rough estimate of strays entering channels

upstream of the Merced River confluence with

the San Joaquin River.}

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San Joaquin River

The San Joaquin River extends l90 miles from its origins in the Sierra Nevada to the town of Vernalis; it drains about 5.9 million acres, including 2 million acres of irrigated farmland. Depending on snow conditions in the Sierra Nevada, peak runoff occurs between late April and August. Stream flow in the upstream stretches of the San Joaquin River is regulated, primarily for temporary storage and direct water diversion, by Millerton Reservoir, behind Friant Dam.

Flows into Millerton Reservoir average an estimated l,762,000 acre-feet annually (all water is used for agriculture, municipal, and industrial purposes, but there are some limited, albeit, incidental environmental benefits). At Millerton, water is diverted into the Friant-Kern and Madera Canals for delivery to water users in Tulare, Madera, Fresno, and Kern Counties. Flow in the San Joaquin River below Friant Dam is limited to the amount needed to meet the State's 5 cubic feet per second requirement at Gravelly Ford to supply riparian water right holders and unauthorized San Joaquin River diverters; between Gravelly Ford and Mendota Pool, there is little or no flow during most years because all available water is used for agriculture or is lost to recharge the overdrafted groundwater aquifer.

The quantity and quality of San Joaquin River water is strongly influenced by the discharge of agricultural drainage. During the irrigation season (March through September), water is imported from the Delta and delivered through the Central Valley Project's Delta-Mendota Canal to the Mendota Pool to supply the Friant Unit's "exchange contractors" along the San Joaquin River, and to the San Luis Reservoir and San Luis Canal to supply the majority of the San Luis Unit contractors. The Mendota Pool also receives some intermittent flow from Fresno Slough. Water from the pool is then delivered northward via the San Joaquin River to Sack Dam. This reach between Mendota Pool and Sack Dam (about 30 miles) has perennial flows from Delta-Mendota Canal's Delta export water deliveries. At Sack Dam, the river is diverted into Arroyo Canal for delivery to various irrigation districts (exchange contractors) and to wetlands in the western Grasslands area. During the irrigation season, between Sack Dam and the mouth of the Merced River, flows in the San Joaquin River consist almost entirely of contaminated agricultural drainwater, primarily resulting from CVP water deliveries to the San Luis Unit.

Irrigation return flows enter the San Joaquin River predominantly from Mud and Salt Sloughs. Average annual discharges are 54,000 acre-feet for Mud Slough and 204,000 acre-feet for Salt Slough. Of these totals, the four northern districts discharge 23,000 acre-feet of tile water commingled with 34,000 acre-feet of surface returns. Irrigation drainwater in Mud and Salt Sloughs accounts for 44 percent of the flow in the San Joaquin River above its confluence with the Merced River in a normal water year (e.g., 1979) (Moore et al. l990). In a dry year (e.g., 1981), Mud and Salt Sloughs account for 70 percent of the flow. The historic contribution of Mud and Salt Sloughs (prior to construction of Friant Dam) to the San Joaquin River flows were below one percent of those total annual flows (SJVDP 1990).

Addition of agricultural drainage water to the San Joaquin River results in reduced water quality (due to accumulations of salt, trace elements such as selenium, and nutrients). In contrast, water quality in the Sierra Nevada streams (the source of historic flows in the lower San Joaquin River and wetlands in the valley) is generally very high. From Friant Dam downstream to Mendota Pool, good water quality is maintained when water is available (only during flood flow releases from Millerton Lake). However, as flows move onto the San Joaquin Valley floor, the quality declines. Due to agricultural return flows and other discharges of urban and municipal wastes, the San Joaquin River carries some of the poorest quality water in the Valley. In the reach of the River just downstream of Sack Dam, which is usually dry due to water diversions, the primary sources of stream flow are irrigation return flows and groundwater discharged either directly or via Mud and Salt Sloughs. During a normal water year, Mud and Salt Sloughs contribute 72 percent of the salt load (and 44 percent of flow) in the San Joaquin River above the mouth of the Merced River. The contribution increases to 80 percent of the salt load and 70 percent of the flow during dry years. These two sloughs contribute 82 percent of the selenium load in this reach of the San Joaquin River.

Fish collected from the sloughs during the mid 1980's showed elevated levels of selenium in their tissues. Aggregate geometric mean (dry weight) selenium concentrations in whole bluegill samples ranged from 4.4 ppm at Salt Slough to 10.4 ppm at Mud Slough (North). Selenium concentrations in freshwater fishes in the United States average 0.5 ppm. It has been estimated that selenium concentrations of 2.0 ppm could cause toxic effects in fish (Saiki 1985, in Moore et al. 1990). Based on data collected during the fall of 1986, (Saiki 1989, in Moore et al. 1990) noted that selenium concentrations in bluegill gonads from samples collected in the western Grasslands area were sufficiently elevated to impair the reproduction of this species.

San Joaquin River water quality improves from the mouth of the Merced River to Vernalis, due to the diluting effects of the Merced, Tuolumne, and Stanislaus Rivers. However, the San Joaquin River still receives nutrients from agricultural drainage that promote algal growth.

Merced River

Flows of the lower Merced River are regulated by the multi-purpose New Exchequer Dam, and by McSwain, Merced Falls, and Crocker-Huffman diversion dams. Several additional riparian and pump diversions are located between Merced Falls Dam and the confluence with the San Joaquin River. The Merced River fish facility, located below New Exchequer Dam near the town of Snelling, was established (as part of the New Exchequer Dam project) to enhance the existing salmon resources in the Merced River. Annual production of fall-run chinook salmon at the hatchery is presently 300,000 yearlings and 400,000 smolts. The Merced has adequate, natural spawning habitat to sustain at least 25,000 returning fall-run salmon (Reynolds et al. 1990). The number of returning fall-run salmon averaged 9,800 individuals in the 1980's, but the populations are on a downward trend with populations equal to or less than those of the endangered winter-run chinook salmon (Appendix A, "Chinook Salmon Spawning Estimates: 1940-1989"). California Department of Fish and Game reported that the 1990, escapement in the Merced River was 73 salmon (49 of these fish were spawned at the Merced Fish Facility near Snelling) with a rough estimate of 280 strays entering San Joaquin River channels upstream of the Merced River. There is no spawning habitat in the San Joaquin River for the stray salmon. Some of these fish are captured at the expense of the State of Calitornia and relocated to the Merced River Fish Facility. The 1992, escapement was reported to be 58 fish (personal communication, Loudermilk 1992).

Because the volume of water (primarily agricultural drainage water) entering the San Joaquin River from Salt Slough can exceed Merced River outflows, many migrating adult salmon are attracted into the sloughs instead of the Merced River. The CDFG installed fish trapping facilities on San Luis Canal in 1988 to handle misguided adult fish, which are transplanted to the Merced River Fish Facility (Moore, et al. 1990). CDFG annually places a barrier across the San Joaquin River channel to provide an additional deterant to misguided salmon.

Stanislaus, Mokelumne, Calaveras, Cosumnes, and Toulumne Rivers salmon population declines are correlated with the construction of Friant Dam, but direct consequences or contributions of Friant Dam construction and water diversions to salmon population declines have not been established. Impoundments and diversions on each river, drainwater discharges, and Delta pumping have likely been much larger factors leading to the abysmal San Joaquin River tributaries' salmon populations. These salmon populations are continuing to decline to the brink of extinction.