DRAFT Raines/D-5820/08/18/92

SUMMARY OF FRIANT FISHERY ISSUES

WITH PRELIMINARY INSTREAM FLOW RECOMMENDATIONS

Fishery issues associated with the Friant Division contract renewals include three general concepts: (1) restoration of a chinook salmon fall-run to the mainstem San Joaquin River (this could eventually lead to restoration of other native fish fauna), (2) aiding salmon production in the San Joaquin River basin drainage by providing flows (controlled freshets) to the lower river during smolt outmigration, and (3) maintaining resident cold-water (trout) and warm-water (bass) fisheries. These issues are described and briefly discussed below presented with some preliminary instream flow requirements.

1. Restoration of a chinook salmon fall-run to the mainstem San Joaquin River below Friant Dam.

Restoration of a salmon run to the upper San Joaquin River (Friant Dam to Merced River confluence) is a problematic concept because of widespread and severe river habitat degradation, and because the fish has a complex life cycle and is vulnerable to impacts in both freshwater and marine systems. Degradation of the San Joaquin River began in the late 1800's and early 1900's and today, many entities (private, local, State and Federal governments) are actively engaged in routing water through an extensive network of canals, bypasses, and diversions. The cumulative effects of these efforts have created a river that is intermittently dry (Gravelly Ford to Mendota Pool (17 miles) and Sack Dam to Salt Slough confluence (54 miles)) and the existing fisheries is dominated by introduced life forms. Naturally producing salmon populations persist in the Merced, Tuolumne, and Stanislaus Rivers with the aid of extensive habitat restoration efforts, including delivery of fishery flows, and artificial propagation.

The following outlines some tasks by life history stage (Table 1) that would/may be necessary to restore a natural salmon run (fall-run) to the San Joaquin River below Friant Dam. This information is presented because simply providing flow in the river will not restore the species. It is assumed, for the present, that the mainstem San Joaquin River could be restored as a migration corridor, however, other migratory routes should not be summarily dismissed and may need further consideration in the future (e.g., the Mariposa/Eastside Bypass system or the Salt Slough/Arroyo Canal system).

Upstream passage (adult migration): determination and provision of flows (general goal of an in-channel water depth ³ 0.5 feet and water velocities £ 2.0 feet per second (fps)) (to include timing and protection of flows - water-rights administration), temperatures (£ 68° F from September 1-November 30 at Vernalis), and other critical water quality variables (e.g., dissolved oxygen, TDS) necessary for adequate upstream passage in the fall (target reach Friant Dam to Merced River confluence); need to better estimate the time it would take for upstream adult migration to the spawning area (15-21 days based on a conservative estimate of swimming speed); rebuild fish ladders at Mendota and Sack Dams (rebuilding fish ladders at Sack and Mendota dams could enable upstream invasion of striped bass to the area below Friant Dam which could eventually impact the success of salmon restoration efforts); provide passage at the Salt Slough control structure; screen or block Mud and Salt Sloughs, Mariposa Bypass and Slough, and other canals, etc. in the fall; estimate predation losses from striped bass (or other species) below dams.

Table 1. Use of the San Joaquin River by life stages of fall-run chinook salmon (CDFG 1987).

Fall-run Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun

Adult

Migration xx xxx xxx xxx

Spawning x xxx xxx xx

Incubation x xxx xxx xxx xxx xxx x

Rearing and

Outmigration x xxx xxx xxx xxx xxx xxx x

Spawning: determine flow (general goal is an in-channel water depth of 1.0-3.0 feet, pool depth of 3.5 to 9 feet, and water velocities of 1.0-3.5 fps), water quality to include temperature (42-57.5° F) needs for the San Joaquin River below Friant Dam to the Gravelly Ford river reach; rebuild and restore spawning areas (specifically about 13 river miles (Friant Dam to Lanes Bridge (Blackstone Avenue)) where some 267,000 square feet of spawning area may remain (this area should be expanded to include the 34 mile river reach from Friant Dam to Skaggs Bridge (Highway 145 or Madera Avenue) where suitable spawning habitat may exist; replace spawning gravels (river channel is narrowed and substrate is anchored due to low flows, sedimentation, and vegetation encroachment).

Incubation and Rearing: determine flow (general flows of 0.3 to 2.4 fps, in-channel depths of 0.5 to 2 feet, and incubation intergravel flows of ³ 26 feet per hour), water quality to include temperature (incubation - 53-57.5° F, and rearing - 53-65° F), and food supply needs for incubation and rearing in the San Joaquin River between Friant Dam and the Gravelly Ford river reach (specifically the Friant Dam to Skaggs Bridge (Highway 145 or Madera Avenue) river reach (34 miles), reduce predation pressure from largemouth bass by isolating (or filling) gravel excavation pits from the mainstem channel; estimate predation pressure from rainbow trout and striped bass.

Downstream passage (outmigration): determination and provision of adequate flows (10,000 cfs flow at Vernalis for a median wet/maximum water year)(to include timing and protection of flows - water-rights administration), temperatures (£ 68° F from April 1-June 30 at Vernalis), and other water quality needs (e.g., dissolved oxygen levels) from below Friant Dam to the Merced River confluence and downstream to the Sacramento-San Joaquin Delta (Delta). Need to better estimate time it takes for a smolt to travel the length of the system and to determine threshold levels for chronic exposure to warm river temperatures, sunlight, irrigation runoff chemicals, and other factors. Need to restore facilities at Mendota and Sack Dams to allow for downstream passage, while reducing potential predation by striped bass. Need to provide passage for smolts at the Sand Slough control structure. Need to screen diversions including mouth of Eastside (Chowchilla) Bypass, Arroyo Canal, riparian diversions, Old River, etc., and so reduce potential entrainment in diversions. Determine flows needed to flush smolts from lower river to avoid losses to entrainment and predation at the pumping facilities in the south Delta.

Passage through the Delta: need to better estimate adequate river flows to offset effects of pumping operations and to aid fish movements toward the ocean. Selenium and other contaminants are potentially detrimental to young salmon in the Delta and regulation of the amounts of these toxicants needs to be more tightly controlled. In general, from August through January, suitable water quality and attractant flows are needed in south Delta channels for adult migration, spawning, and outmigration.

Ocean/river harvest: should consider the possible reduction of ocean and river harvests, at least during initial restoration efforts, to allow establishment and stabilization of salmon populations.

Hatcheries/Artificial Propogation: the need for hatchery supplementation/propogation may be necessary if production goals are not achieved or if accessibility to spawning areas is limited and/or to maintain genetic material from the race (e.g., maintenance of a "vital thread"). The need for hatcheries is not well established and might not be until other restoration actions are taken and evaluated. Trapping, relocation (hauling), and artificial propagation should be considered for critical and dry water years in the basin (e.g., Salt Slough trap and haul operation currently employed in the basin).

San Joaquin River flow needs: definitive flow needs of fall-run chinook salmon (for life stage use from Table 1) in the San Joaquin River are not entirely known, and in lieu of conducting a detailed instream flow analysis at this time (e.g., using the US Fish and Wildlife Service's Instream Flow Incremental Methodology (IFIM) which may not be wholly appropriate for the current assessment, various information sources can be used to obtain a general idea of salmon flow needs for the San Joaquin River. These flow needs are summarized and discussed below under items (a), (b), and (c) presented below.

(a) Table 2 presents minimum flow requirements as reported (and repeated) in various State and Bureau of Reclamation (Reclamation) documents. The minimum flow requirements reported were developed during the late 1950's.

Table 2. San Joaquin River flow - fall-run restoration minimum flow requirements.

Below Below "White- "White- Mendota Mendota Below Below

Friant Friant house" house" Pool to Pool to Sack Sack

Dam Dam Gage Gage Sack Dam Sack Dam Dam Dam

Month (CFS)¹ (TAF/mo)² (CFS)³ (TAF/mo) (CFS)⁴ (TAF/mo) (CFS)⁵ (TAF/mo)

Oct 350 21 185 11 185 11 150 9

Nov 350 21 185 11 185 11 150 9

Dec 350 21 185 11 185 11 150 9

Jan 200 12 200 12 150 9 100 6

Feb 200 12 200 12 150 9 100 6

Mar 150 9 150 9 100 9 100 6

Apr 100 6 100 6 100 6 100 6

May 100 6 100 6 100 6 100 6

Jun-Sep 0 0 0 0 0 0 0 0

TOTAL/YR - 108 - 78 - 72 - 57

¹Cubic feet per second; corresponds to USGS gaging station 11251000.

²Thousand acre-feet/month.

³Corresponds to Bureau of Reclamation gaging station "Gravelly Ford".

⁴Corresponds to USGS gaging station 11254000.

⁵Corresponds to USGS gaging station 11256000.

The fishery agencies (Federal and State) generally agree that these minimum flow requirements are probably inaccurate for present river conditions, particularly those during spring and summer. However, they can be used as a guide in developing new instream flow recommendations reflecting present-day conditions. These flow recommendations were developed based on known chinook salmon use of the river, albeit primarily spring-run chinook salmon use, during the 1940's and 1950's.

(b) Table 3 presents minimum flow requirements as extra- polated from a somewhat similar drainage, the Tuolumne River. For a comparison, the unimpaired runoff (1906-1989) in the San Joaquin drainage for the Tuolumne River is calculated to be 33.2 percent of the total. The upper San Joaquin River is calculated to contribute 30.4 percent. These two rivers are geophysically very similar.

The 1964 flow estimates presented in Table 3 were obtained from preliminary efforts with instream flow analyses and are reported in California Department of Fish and Game, Exhibit 15, Appendix 5B ("The status of San Joaquin drainage chinook salmon stocks, habitat conditions and natural conditions and natural production factors", CDFG, 1987). The fishery agencies considered these flows to be inadequate to maintain natural salmon populations and more recent flow estimates are reported in column 2 (1992 flow estimates).

These estimates are reported in the Agreement between Turlock and Modesto Irrigation Districts and California Department of Fish and Game (Article 39, FERC Project No. 2299) that was initiated March 1, 1992 (Attachment 1). The flows represent a long-term average type of water year equating to an inflow into Don Pedro Reservoir of between 1,325,000 acre-feet and 1,765,000 acre-feet (i.e., intermediate BN-AN in referenced report). The long-term average inflow (1922-1980) into Millerton Lake is approximately 1,700,000 acre-feet which would equate to a similar water year type.

It should be emphasized that these 1992 flow estimates are preliminary and represent the fishery agencies "best guess" at this time. Flows for eleven identified/defined water years were established (Attachment 1). Flows for five water year types for the Tuolomne River, of interest for the upper San Joaquin River, are presented in Attachment 2. Attachment 3 contains information explaining and defining the five water year types to be used for the San Joaquin basin. Please refer to this attachment for more information.

The Tuolomne River flow estimates are useful in that they can be used as a comparison, and guide, for the development of upper San Joaquin River water year specific instream flows. The fishery agencies believe that the life requisites of fall-run chinook salmon will be better met with the 1992 flows than with the 1962 flows.

Table 3. Minimum flow requirements for the Tuolomne River at La Grange bridge (river mile 50.5).

1964 1992 1992

Estimates Estimates Acre-Foot

Period (CFS) (CFS) Estimates

Pre-season

flushing flow 2,500 - -

(discretionary)

October (31)¹ 200 (Oct 1-15) 225 (Oct 1-14) 6,300

250 (Oct 16-31) 1,075 (Oct 15-16) 4,300

200 (Oct 17-31) 6,000

November (30) 385 200 12,000

December (31) 385 (Dec 1-15) 200 (Dec 1-31) 12,000

280 (Dec 16-31)

Jan-Feb (59) 280 200 23,600

March (31) 350 200 12,400

April (30) 100 250 (Apr 1-21) 10,500

950 (Apr 22) 1,900

2,135 (Apr 23-30) 34,160

May (31) 3 2,135 (May 1-13) 55,510

925 (May 14) 1,850

250 (May 15-31) 8,500

Jun-Sep (122) 3 100 (Jun - Sep) 24,400

TOTALS - - 213,420

¹Number of days in flow period.

(c) Historical flows for times when fall-run (and spring-run) adults were observed in the San Joaquin River (spawning migrations) before Friant Dam was in full operation, e.g., years between 1939 and 1948, can be used to describe the natural flow regime of the San Joaquin River and indicate flow conditions that supported and sustained migrating and spawning salmon. Hydrological information (pre- and post-Friant flow records for selected gaging stations) were available for the San Joaquin River. A comparison of the pre- and post-Friant flows (specifically salmon ascending and descending flows) was made (using flow data in a period of record from 1908 to 1992, but specifically 1940 to 1954).

Table 4 presents the US Geological Survey (USGS) gaging station information for the period 1940 through 1954 for the San Joaquin River between Friant Dam and Dos Palos, downstream of Sack Dam (river reaches of: (1) Friant Dam to Mendota Pool (63 miles); Mendota Pool to Sack Dam (23 miles); and Sack Dam to the Merced River confluence (64 miles)), for spring-run upstream and fall-run up- and downstream chinook salmon migratory months. Spring-run chinook salmon numbers entering the upper San Joaquin River above Fresno are also presented. Generally, only sparse or incomplete records of fall-run spawners are available; the fall-run population averaged about 1,000 spawners in the 1940's.

It can be inferred from Table 4 that there never was much of a fall-run in the upper San Joaquin River due mainly to the flow situation in the Sack Dam to Merced River confluence river reach. Most years the flow in this river reach approached zero. Those years where a large spring-run count was made, upstream passage flows were available in the Sack Dam to Merced River confluence river reach. Since 1949 river flows have approached zero in this river reach thereby basically eliminating the spring- and fall-runs.

It should be noted that between 1940 and 1952, there were seven median dry to median below normal water years, five median below normal to median above normal water years, and three median above normal to median wet/maximun water years (Millerton Lake inflows for seven of the fifteen water years were above the long-term average). Spring-run chinook salmon counts were greatest for water years corresponding to median below normal to median wet/maximum.

It would appear that the limiting factor for successful upper San Joaquin River chinook salmon restoration is passage related, and not particularly related to flows for spawning, egg incubation, and rearing. The two intermittant river reaches must become perrenial during upstream spawning migration and during outmigration.

In an attempt to better understand the current flow patterns of the upper San Joaquin River below Friant Dam (1976 through 1991) and relate fall-run chinook salmon use to them, it was believed that understanding the stage-discharge relationship for specific river reaches would be helpful. This relationship could be used to help determine life-stage suitability for fall-run chinook salmon (passage as well as spawning, egg incubation, and rearing) by comparing flows and channel morphology to suitability curves, by life stage, which have been developed for chinook salmon by the US Fish and Wildlife Service (Habitat Suitability Index Models and Instream Flow Suitability Curves: Chinook Salmon, Biological Report 82(10.122), September 1986).

Table 4. San Joaquin River mean monthly flows and chinook salmon spawning counts between Friant Dam and the downstream of the Sack Dam (Dos Palos gaging station) for the adult upstream spawning migration period (spring-run - April, May, June; fall-run - September, October, November) 1940

through 1954.

Spring- USGS

run Gaging Mean Monthly Flows (CFS)

Year Count¹ Station² April May June Sept. Oct. Nov.

1940³ N/A 11251000 4189 6618 5564 1069 784 760

11254000 3156 5552 3840 10 30 241

11256000 - - - - 0 0

1941⁴ 9,000 11251000 3846 9107 9438 1298 968 817

11254000 4764 8680 10350 200 223 448

11256000 4633 7390 8179 0 0 206

1942⁴ N/A 11251000 4702 6394 8032 1306 1019 1116

11254000 3572 4638 8317 196 294 784

11256000 3316 4190 7312 0 0 553

1943³ 35,000 11251000 5083 6211 4652 1166 961 823

11254000 5392 4862 3436 148 189 238

11256000 4894 4241 3118 0 0 0

1944⁵ 5,000 11251000 2131 1984 2178 1965 1300 550

11254000 302 286 479 287 278 183

11256000 0 66 183 5 28 42

1945³ 56,000 11251000 4264 5166 4628 1995 1663 1442

11254000 2574 4438 3705 394 637 1144

11256000 2285 3745 3146 169 421 916

1946³ 30,000 11251000 2165 4605 3431 1900 1428 529

11254000 362 2708 1225 274 252 271

11256000 92 2265 1021 5 11 129

1947⁵ 6,000 11251000 2480 2113 2282 1630 999 410

11254000 315 374 421 234 139 105

11256000 55 118 120 2 1 0

1948⁵ 2,000 11251000 1087 1897 2065 2392 1234 415

11254000 162 234 244 329 206 70

11256000 45 20 3 4 1 0

1949⁵ No count 11251000 2471 2019 2928 1612 1024 382

11254000 287 228 329 227 105 46

11256000 3 4 4 1 0 0

1950⁵ No fish 11251000 1884 1937 2318 1563 989 278

11254000 240 227 326 227 168 555

11256000 2 2 4 0 1 397

1951³ - 11251000 2000 1713 2169 352 591 417

11254000 255 200 287 177 139 93

11256000 4 3 3 1 1 0