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 The Stanislaus River Restoration Plan Information Site

Carl Mesick Consultants
El Dorado, California 95623

The California Rivers Restoration Fund
Soulsbyville, Ca. 95372

and

S.P. Cramer & Associates, Inc.
Chico, California 95928

Participating Agencies/Organizations Include:

U.S. Fish and Wildlife Service, California Department of Fish and Game, California Department of Water Resources, NOAA Fisheries, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation, and other organizations conducting research in the Stanislaus River.

The Stanislaus River stakeholders and local citizenry have worked together to develop this restoration plan in an adaptive management context to effectively facilitate restoring ecosystem processes and habitats to benefit at-risk fish species, including Chinook salmon and steelhead in the Stanislaus River downstream from Goodwin Dam. The primary purpose of this plan is to provide guidance for all interested parties on the design, implementation, and monitoring of proposed restoration projects and directed research programs in the lower Stanislaus River.

The plan is envisioned as a "living document" that will need to be periodically updated as we learn from ongoing and future restoration projects throughout the Central Valley. As the plan is developed and updated, it will be posted on websites created by S.P. Cramer & Associates, the California Rivers Restoration Fund, and the Anadromous Fish Restoration Program to encourage comments from stakeholders and the local citizens. It is anticipated that additional funding will be provided to periodically update the plan.

1.1 BACKGROUND:

1.1.1 Stanislaus River Fish Group:

The Stanislaus River Fish Group consists of representatives of the U.S. Fish and Wildlife Service, California Department of Fish and Game, California Department of Water Resources, NOAA Fisheries, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation, California Rivers Restoration Fund, and other organizations conducting research in the Stanislaus River: including S.P. Cramer and Associates, Inc., Carl Mesick Consultants, Fisheries Foundation, and the University of California at Berkeley. The Stanislaus River Fish Group has been meeting to exchange information and discuss fishery management issues since 1996.

1.1.2 Purpose and Need for Restoration Plan:

Although other fishery restoration plans have been written for the lower Stanislaus River over the past decade, few restoration actions or studies have been implemented to date. One reason for the lack on progress on the lower Stanislaus River is the lack of a local-level consensus-based plan. The previous restoration plans that were developed for Central Valley Rivers, including the lower Stanislaus River, were all produced by government resource agencies:

• Department of Fish and Game's 1993 Restoring Central Valley Streams: A Plan for Action;
  
• U.S. Fish and Wildlife Service's 2000 Final Anadromous Fish Restoration Plan;
  
• U.S. Fish and Wildlife Service's 1998 Central Valley Project Improvement Act Tributary Production Enhancement Report; and
  
• CALFED's 1999 Ecosystem Restoration Program Plan.

Unlike the previous plans, this restoration plan is the first to be developed specifically for the lower Stanislaus River by all stakeholders and the local citizenry. Both the Anadromous Fish Restoration Program (AFRP) and the CALFED Bay Delta Program (CALFED) emphasize the need to work with all stakeholders and the local citizenry to develop restoration plans in an adaptive management context to restore processes and habitats that benefit at-risk fish species, including Chinook salmon and steelhead in the Central Valley.

Another reason for the lack of progress restoring the lower Stanislaus River is that only the CALFED plan had undergone an external review by restoration experts. It is anticipated that additional funding will be provided for an external review of this plan.

A third reason is that none of the previous plans provided guidance as to the design, implementation and monitoring of potential projects. Although there has been agreement as to the type of action needed, there has been disagreement regarding the proposed methods or design of restoration projects. This plan will provide consensus-based recommendations for the design, implementation, and monitoring for all actions designated as a high-priority.

1.1.3 Funding and Preparation:

The AFRP has provided partial funding for Carl Mesick Consultants, the California Rivers Restoration Fund, and S.P. Cramer and Associates, Inc. to produce the initial plan with the input of all stakeholders and the local citizenry. Carl Mesick Consultants, S.P. Cramer and Associates, Inc., and the California Rivers Restoration Fund have donated a substantial amount of time and materials toward the completion of this plan.

1.2 SCOPE OF RESTORATION PLAN:

The Stanislaus River is one of three tributaries to the San Joaquin River (Figure 1). Its watershed is about 1,100 square-miles in which most of the precipitation falls between November and April near the headwaters (Kondolf and others 2001). The average unimpaired basin runoff is approximately 1,200 thousand acre-feet (TAF), which is slightly more than half of the averages for the Tuolumne River (33.2% of San Joaquin basin total) and upper San Joaquin River (30.2% of San Joaquin basin total).

1.2.1 Lower Stanislaus River:

This plan focuses on the 58.3-mile reach of the Stanislaus River between Goodwin Dam and the confluence with the San Joaquin River (Figure 1). Currently, anadromous fish cannot migrate upstream of Goodwin Dam.

1.2.2 Anadromous Fish Species of Primary Concern:

This plan focuses on the restoration of habitat for two species of anadromous fish: Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss irideus). Anadromous fish spend most of their lives in the sea and migrate as adults to spawn in fresh water. Steelhead and spring-run Chinook salmon in the lower Stanislaus River and elsewhere in the Central Valley are listed as threatened under the federal Endangered Species Act of 1973. Spring-run Chinook salmon are also listed under the California Endangered Species Act. Fall-run Chinook salmon in the Stanislaus River and elsewhere in the Central Valley are candidates for listing under the federal Endangered Species Act. It is unlawful for government agencies or private entities to kill, injure, harm, or harass listed species without permits from NOAA Fisheries. Even observing and handling listed species of anadromous fish for the purpose of scientific studies requires permits from NOAA Fisheries.

Other anadromous fish species that occur in the lower Stanislaus River include striped bass (Morone saxatilis), American shad (Alosa sapidissima), and an unidentified species of lamprey. Striped bass and American shad were introduced into the Sacramento-San Joaquin basin in the late 1880s. None of these species are considered to be threatened.

Historical Accounts:

Historically, spring-run, fall-run and possibly late fall-run Chinook salmon (Yoshiyama and others 1996) and steelhead trout (Yoshiyama and others 1998) occurred in the Stanislaus River. The California Department of Fish and Game (CDFG) speculated that historically the spring-run was the primary salmon run in the Stanislaus River, but after Goodwin Dam blocked upstream migration sometime between 1913 and 1929, the fall-run population became dominant (in Yoshiyama and others 1996). Records on late fall-run Chinook salmon and steelhead trout in the San Joaquin tributaries are sparse (Yoshiyama and others 1998).

Goodwin Dam, which was completed in 1913, is approximately 58.3 miles upstream from the confluence of the Stanislaus River with the San Joaquin River. Clark (1929) reported that there was a fish ladder at Goodwin Dam and that anadromous fish used to spawn upstream of the dam. However, Hatton (in Yoshiyama and others 1996) stated in 1940 that the Goodwin Dam ladder was "seldom passable" and that the fluctuating water level caused by hydroelectric operations above the dam made it "very nearly an impassable barrier". Hydroelectric operations that made the ladder ineffective may have begun with the completion of Old Melones dam in 1926. Fry (1961) also reported that Goodwin Dam was a barrier to migration after CDFG began its salmon escapement surveys in 1940.

Salmon and steelhead were abundant in the Merced and Tuolumne rivers and presumably the Stanislaus River as well prior to 1849 when the Gold Rush began; however, the runs probably declined rapidly thereafter (Yoshiyama and others 1996, 1998). The California Fish Commission stated in 1886 (in Yoshiyama and others 1996): "The Tuolumne, a branch of the San Joaquin, at one time was one of the best salmon streams in the State. Salmon have not ascended the stream for some years". A U.S. Army officer in the San Joaquin basin wrote in the 1860s that he expected a poor salmon run in the San Joaquin River and its tributaries as a result of low flows and sedimentation from hydraulic mining (Mesick, personal communication, see "Notes"). Clark similarly reported in 1929 that "[t]he abundance of salmon in the Stanislaus is about the same as in the Tuolumne" and "that salmon in the Tuolumne are scarce". He further reported that "[t]he spring run amounts to almost nothing, but there are some fish that come up the stream in the fall."

It is likely that hydraulic mining caused the initial decline of the salmon and steelhead runs in the Stanislaus River, because the early dams were too small to substantially affect streamflows and they did not completely block the salmon's upstream migration until Old Melones Dam was constructed in 1926. The earliest "permanent" dam on the river, which was the original Tulloch Dam constructed in 1858, was a relatively low structure that had an opening at one end (Yoshiyama and others 1996). Miwok residents caught salmon upstream of the original Tulloch Dam at Burns Ferry Bridge and Camp Nine between 1870 and 1920 (Yoshiyama and others 1996) and so the construction of dams alone cannot account for the initial declines. On the other hand, hydraulic mining, which occurred in California between 1853 and 1884, is evident near Columbia and to a small degree near Knights Ferry in the Stanislaus River watershed.

Since 1940, when CDFG began estimating the number of fall-run Chinook salmon that returned to spawn in the San Joaquin tributaries each year, the abundance of fall-run salmon in the Stanislaus River has ranged between 100 and 35,000 fish (Fry 1961, Mesick 2001a). Since 1940, their abundance has been significantly correlated with the abundance of spawners and springtime flows when the juvenile fish migrated to the ocean (Mesick 2001a).

In recent years, up to about 100 spring-run salmon have been observed in the Stanislaus River annually. These fish typically migrate into the river between mid-February and July (CDFG 1998) and hold in deep water in Goodwin Canyon downstream to the Orange Blossom Bridge until they spawn in September and October. One location where they have been routinely observed in the last several years is a deep, gravel pit at the U.S. Army Corps of Engineers' Button Bush Park, which is about one mile upstream from the Orange Blossom Bridge. In summer 2000, CDFG used gill nets to capture 22 of these fish in Button Bush Park and determined that three had coded-wire tags identifying them as strays from the Feather River Hatchery (Fisheries Foundation 2002).

Large Oncorhynchus mykiss irideus are caught by anglers in the Stanislaus River primarily between January and April, and it is likely that some of these fish are anadromous steelhead trout whereas others are probably resident rainbow trout. Although the anadromous nature of the large trout has not been confirmed by extensive studies of strontium concentrations in otoliths or ocean growth patterns in scales, there are several characteristics of these fish that make it likely that many are steelhead:

• Scales taken from trout larger than 20 inches in length indicate a period of accelerated growth that is typical of estuary or ocean residence (McEwan 2001).
  
• Large adult fish weighing up to about 5.6 kilograms (12.25 pounds) are primarily caught during the typical period that adult steelhead migrate into Central Valley tributaries to spawn (Walser, personal communication, see "Notes").
  
• Some of the large fish have a bright silvery body and red color on their operculum, which is typical of steelhead that have just entered fresh water (Walser, personal communication, see "Notes").
  
• Some of the large adults have lice, which may be a species found in the Delta (Bill Mitchell, personal communication, see Notes), that suggests that the fish either reside or migrate through the Delta.
  
• A few juvenile trout have characteristics typical of steelhead smolts migrating to the ocean: they are approximately 200 mm in length, have a smolt index of 5 based on the IEP Steelhead Project Work Team Steelhead Life-stage Assessment Protocol, and are caught in screw traps at Oakdale and Caswell Park between January and June each year (Demko and others 2000).
  
• A genetic analysis of steelhead smolts captured in rotary screw traps on the Stanislaus River indicate that they are closely related to the upper Sacramento River steelhead, but not steelhead from the Mokelumne River Hatchery or Nimbus Hatchery on the American River (McEwan 2001) and so they appear to be a population of naturally produced fish.

Although the abundance of steelhead is not surveyed in the Stanislaus River, the catch of adult steelhead using hook-and-line began to increase in 1997, when many fish between 12 and 15 inches were caught. The catch increased again in 1999, when both the number and size (2 to 10 pounds) of the fish caught increased (Walser, personal communication, see "Notes"). High catch rates have continued through 2002.

2.1 PURPOSE OF THE PUBLIC OUTREACH PLAN:

The initial outreach will be conducted by the California Rivers Restoration Fund and S.P. Cramer and Associates, Inc. to inform the public, affected parties, and other stakeholders about the restoration plan, its ongoing status, and to provide the opportunity to provide input on the development of the plan.

2.2 TARGET AUDIENCE:

The primary target audience for outreach will include all residents and recreational users of the lower Stanislaus River between Goodwin Dam and the confluence with the San Joaquin River, local government agencies, non-profit environmental and recreational organizations, and the local irrigation and water districts that obtain water from the Stanislaus River.

2.3 METHODS:

A variety of tools, including meetings, newspaper announcements, Internet websites, and newsletters, will be used to conduct outreach throughout the development of the plan. In addition to the regular meetings of the Stanislaus River Fish Group and posting the restoration plan on the Internet, public meetings will be held at Knights Ferry and Oakdale to discuss the development of the restoration plan and to provide contact information. Notices of upcoming public meetings, contact information, and background information on the restoration plan will be published in the local newspapers (Oakdale Leader, Modesto Bee, and The Record), Internet message boards of California-based sport fishing groups, newsletters of participating organizations/agencies, and on web pages of the California Rivers Restoration Fund, S.P. Cramer and Associates, Inc., and the AFRP. The California Rivers Restoration Fund will link its website (www.calriversfund.org) with other non-profit organizations, such as California Trout, whereas S.P. Cramer and Associates, Inc., (www.stanislausriver.com) and Stanislaus River Fish Group have linked their websites with those of other resource agencies, such as the CALFED Bay-Delta Program and the Department of Fish and Game. The Stanislaus River Fish Group page can be accessed through the Partners link at the AFRP site (www.delta.dfg.ca.gov/afrp/afrp.asp).

2.4 SUMMARY OF COMMENTS:

This section will present a summary of all outreach related comments received on the restoration plan and responses to the comments.

3.1 OVERVIEW:

The lower Stanislaus River has been extensively developed to provide water, hydroelectric power, gravel, and conversion of floodplain habitat for agricultural and residential uses. Developments in the lower San Joaquin River and Delta that may affect anadromous fish as they migrate between the Stanislaus River and the ocean are also discussed.

3.2 WATER AND HYDROELECTRIC PROJECTS:

The 32 dams within the Stanislaus basin large enough to be regulated by the Division of Safety of Dams have a total capacity of 2,846,500 acre-feet or 237% of the average unimpaired runoff. New Melones dam, which was completed in 1979 and approved for filling in 1981, has a storage capacity of 2,400,000 acre-feet and was designed to control floods up to the 100-year-flood (Kondolf and others 2001).

The operating criteria for New Melones Reservoir are governed by water rights, instream fish and wildlife flow requirements (including AFRP objectives), Bay-Delta flow requirements, dissolved oxygen requirements, Vernalis water quality, CVP contracts, and flood control considerations. Water released from New Melones Dam and Powerplant is re-regulated at Tulloch Reservoir, and is either diverted at Goodwin Dam or released from Goodwin Dam to the lower Stanislaus River.

Flows in the lower Stanislaus River serve multiple purposes. These include provision of water for riparian water rights, instream fishery flow objectives, and instream dissolved oxygen (DO). In addition, water from the Stanislaus River enters the San Joaquin River, where it contributes to flow and helps improve water quality conditions at Vernalis. State Water Resources Control Board Decision (D)-1422, issued in 1973, provided the primary operational criteria for New Melones Reservoir and permitted USBOR to appropriate water from the Stanislaus River for irrigation and M&I uses. D-1422 requires that the operation of New Melones Reservoir include releases for existing water rights, fish and wildlife enhancement, and the maintenance of water quality conditions on the Stanislaus and San Joaquin rivers.

3.2.1 New Melones Interim Plan of Operation:

Proposed CVP operations on the Stanislaus River are derived from the New Melones Interim Plan of Operation (NMIPO). The NMIPO was developed as a joint effort between USBOR and USFWS, in conjunction with the Stanislaus River Basin Stakeholders (SRBS). The process of developing the plan began in 1995 with a goal to develop a long-term management plan with clear operating criteria. In 1996, the focus shifted to development of interim operations plans for 1997 and 1998. At an SRBS meeting on January 29, 1997, a final interim plan of operation was agreed to in concept. The NMIPO was transmitted to the SRBS on May 1, 1997. Although meant to be a short-term plan, it continues in effect. In summary, the NMIPO defines categories of water supply based on storage and projected inflow. It then allocates annual water release for fishery, water quality, Bay-Delta, and use by CVP contractors (Tables 3.2.1-1 and 3.2.1-2).

Table 3.2.1-1 Inflow characterization for the New Melones Interim Plan of Operation:

Table 3.2.1-1 Inflow characterization for the New Melones Interim Plan of Operation
Annual water supply category	March-September forecasted inflow plus end of February storage (thousand acre-feet)
Low	0 - 1400
Medium-low	1400 - 2000
Medium	2000 - 2500
Medium-high	2500 - 3000
High	3000 - 6000

Table 3.2.1-2 New Melones Interim Plan of Operation flow objectives (in thousand acre-feet)
Storage plus inflow		Fishery		Vernalis water quality		Bay-Delta		CVP contractors
From	To	From	To	From	To	From	To	From	To
1400	2000	98	125	70	80	0	0	0	0
2000	2500	125	345	80	175	0	0	0	59
2500	3000	345	467	175	250	75	75	90	90
3000	6000	467	467	250	250	75	75	90	90

3.2.2 Water Rights Obligations:

When USBOR began operations of New Melones Reservoir in 1980, the obligations for releases to meet downstream water rights were defined in a 1972 Agreement and Stipulation among USBOR, OID, and SSJID. The 1972 Agreement and Stipulation required that USBOR release annual inflows to New Melones Reservoir of up to 654,000 acre-feet per year for diversion at Goodwin Dam by OID and SSJID, in recognition of their water rights. Actual historical diversions prior to 1972 varied considerably depending upon hydrologic conditions. In addition to releases for diversion by OID and SSJID, water is released from New Melones Reservoir to satisfy riparian water rights for agricultural irrigation totaling approximately 48,000 acre-feet annually downstream of Goodwin Dam.

In 1988, following a year of low inflow to New Melones Reservoir, the Agreement and Stipulation among USBOR, OID, and SSJID was superseded by an agreement that provided for conservation storage by OID and SSJID. The new agreement required USBOR to release New Melones Reservoir inflows of up to 600,000 acre-feet each year for diversion at Goodwin Dam by OID and SSJID. In years when annual inflows to New Melones Reservoir are less than 600,000 acre-feet, USBOR provides all inflows plus one-third the difference between the inflow for that year and 600,000 acre-feet per year. The 1988 Agreement and Stipulation created a conservation account in which the difference between the entitled quantity and the actual quantity diverted by OID and SSJID in a year may be stored in New Melones Reservoir for use in subsequent years.

Tri-Dam Project and Stockton East Water District Reservoirs

The Tri-Dam project is a partnership between the Oakdale Irrigation District (OID) and the South San Joaquin Irrigation District (SSJID) that was formed in 1948. Tri-Dam was formed to develop, operate and maintain the Beardsley/Donnells project on the middle fork of the Stanislaus River and the Tulloch project downstream of New Melones Reservoir for water storage and power generation. The Beardsley/Donnells project can store about 160,000 acre-feet of water and the Tulloch Project can store about 67,000 acre-feet of water. OID, SSJID, and the Stockton East Water District (SEWD) also own Goodwin Dam, which is just downstream of Tulloch. Goodwin, which can store up to 500 acre-feet of water, is the point of diversion for water for all three districts. It has no hydropower generating facilities. OID and SSJID also obtain water by recapturing drainage water and pumping from deep wells. The water is currently used to irrigate about 144,000 acres of land within the Districts. The irrigated land supports almonds, peaches, apples, walnuts and other crops.

The Beardsley/Donnells and Tulloch projects combined produce about 533,000,000 kwh of power annually. The Tulloch Powerhouse is operated primarily as a run-of-river operation and the Tulloch Reservoir also serves as an afterbay for the New Melones Powerhouse. OID and SSJID also own and operate the Sand Bar Project, which is purely a hydroelectric project located downstream of the Beardsley Afterbay Dam; it generates about 73,000,000 kwh annually. The power is sold to PG&E with the revenues used to: 1) pay off the bonds used to finance the projects; 2) maintain the power project facilities; 3) maintain and improve the water delivery system; and 4) offset the increasing cost of water for their customers.

3.2.3 Instream Flow Requirements:

Under D-1422, USBOR is required to release up to 98,000 acre-feet of water per year from New Melones Reservoir to the Stanislaus River on a distribution pattern to be specified each year by CDFG for fish and wildlife purposes. In 1987, an agreement between USBOR and CDFG provided for increased releases from New Melones to enhance fishery resources for an interim period, during which habitat requirements were to be better defined and a study of Chinook salmon fisheries on the Stanislaus River would be completed. During the study period, releases for instream flows would range from 98,300 to 302,100 acre-feet per year. The exact quantity to be released each year was to be determined based on storage, projected inflows, projected water supply and water quality demands, and target carryover storage. Because of dry hydrologic conditions in the 1987 to 1992 drought period, the ability to provide increased releases was limited. USFWS published the results of a 1993 study, which recommended a minimum instream flow on the Stanislaus River of 155,700 acre-feet per year for spawning and rearing (Aceituno 1993).

3.2.4 Anadromous Fish Restoration Plan Flows:

AFRP flow volumes on the Stanislaus River, as part of the NMIPO, are based on the New Melones end-of-February storage plus forecasted March to September inflow as shown in the NMIPO (Tables 3.2.1-1 and 3.2.1-2). The AFRP volume is then initially distributed based on modeled AFRP distributions and patterns used in the NMIPO. Actual flows below Goodwin Dam will be determined in accordance with Attachment 2 of the Department of the Interior Decision on Implementation of Section 3406 (b)(2) of the Central Valley Project Improvement Act October 5, 1999.

3.2.5 Bay-Delta Vernalis Flow Requirements:

D-1641 sets San Joaquin River at Vernalis flow requirements from February to June. These flows are commonly known as San Joaquin River base flows. USBOR has committed to provide these flows during the interim period of the Bay-Delta Accord. The NMIPO describes the commitment USBOR has made regarding the operation of New Melones Reservoir. If the NMIPO does not commit resources to this objective and the objective is at risk of non-compliance, USBOR will pursue other strategies (for example, water purchases) to meet the base flow commitment.

3.2.6 Dissolved Oxygen Requirements:

D-1422 requires that water be released from New Melones Reservoir to maintain DO standards in the Stanislaus River. The 1995 revision to the Water Quality Control Plan (WQCP) established a minimum DO concentration of 7milligrams per liter (mg/l), as measured on the Stanislaus River near Ripon.

3.2.7 Vernalis Water Quality Requirement:

D-1422 also specifies that New Melones Reservoir be operated to maintain an average monthly level of conductivity, commonly measured as total dissolved solids (TDS), on the San Joaquin River at Vernalis as it enters the Delta. D-1422 specifies an average monthly concentration of 500 parts per million (ppm) TDS for all months. Historically, releases have been made from New Melones Reservoir for this standard, but due to shortfalls in water supply, USBOR has not always been successful in meeting this objective. In the past, when sufficient supplies were not available to meet the water quality standards for the entire year, the emphasis for use of the available water was during the irrigation season, generally from April through September. D-1641 modified the water quality objectives at Vernalis to include the irrigation and non-irrigation season objectives contained in the 1995 Bay-Delta WQCP. The revised standard is an average monthly conductivity 0.7 microSiemens per centimeter (approximately 455 ppm TDS) during the months of April through August, and 1 mS/cm (approximately 650 ppm TDS) during the months of September through March.

3.2.8 Hydropower Operations:

New Melones Powerplant operations began in 1979. The powerhouse is rated at 300 MW. Power generation occurs when reservoir storage is above the minimum power pool of 300,000 acre-feet. When possible, reservoir levels are maintained to provide maximum energy generation.

3.2.9 Flood Control:

New Melones Reservoir flood control operation is coordinated with the operation of Tulloch Reservoir. The flood control objective is to maintain flood flows at the Orange Blossom Bridge at less than 8,000 cfs. When possible, however, releases from Tulloch Dam are maintained at levels that would not result in downstream flows in excess of 1,250 cfs to 1,500 cfs because of potential damage to permanent crops in the floodplain that may occur at flows above this level. Up to 450,000 acre-feet of the 2.4 million acre-foot storage volume in New Melones Reservoir is dedicated for flood control and 10,000 acre-feet of Tulloch Reservoir storage is set aside for flood control. Based upon the flood control diagrams prepared by USACE, part or all of the dedicated flood control storage may be used for conservation storage, depending on the time of year and the current flood hazard.

3.2.10 CVP Contracts:

USBOR has entered into water service contracts for the delivery of water from New Melones Reservoir, based on a 1980 hydrologic evaluation of the long-term availability of water in the Stanislaus River Basin. Based on this study, USBOR entered into a long-term water service contract for up to 49,000 acre-feet per year of water annually (based on a firm water supply), and two long-term water service contracts totaling 106,000 acre-feet per year (based on an interim water supply). Because diversion facilities were not yet fully operational and water supplies were not available during the 1987 to 1992 drought, no water was made available from the Stanislaus River for delivery to CVP contractors prior to 1992.

3.2.11 San Joaquin River Agreement:

Adopted by the SWRCB in Water Rights Decision 1641, the San Joaquin River Agreement (SJRA) includes a 12-year experimental program providing for flows and exports in the lower San Joaquin River during a 31-day pulse flow period during April-May. It also provides for the collection of experimental data during that time to further the understanding of the effects of flows, exports, and the barrier at the head of Old River on salmon survival. This experimental program is commonly referred to as the Vernalis Adaptive Management Program (VAMP).

An Environmental Impact Statement/Environmental Impact Report (EIS/EIR) is prepared annually for the water acquisition (flow) portion of the SJRA. Within the SJRA, the NMIPO has been assumed to form part of the basis for which flows will be provided on the San Joaquin River to meet the target flows for the 31-day pulse during April-May. Additional flows to meet the targets will be provided from other sources in the San Joaquin River under the control of the parties to the SJRA.

The operations forecasts include Vernalis flows that meet the appropriate pulse flow targets for the assumed hydrologic conditions. The flows in the San Joaquin River upstream of the Stanislaus River are forecasted for the assumed hydrologic conditions. These flows are then adjusted so that when combined with the forecasted Stanislaus River flow based on the NMIPO, they provide the appropriate Vernalis flows consistent with the pulse flow target identified in the SJRA. An analysis of how the flows are produced upstream of the Stanislaus River is included in the SJRA EIS/EIR.

3.2.12 Release Temperatures From New Melones Dam:

The presence of Old Melones Dam within New Melones Reservoir causes the release of warm surface water from New Melones Reservoir whenever storage levels fall below about one million acre-feet, a problem that occurred in 1991 and 1992 (Loudermilk 1996). In addition, Tulloch Reservoir can be warmer than 56 oF through the end of October although cold water releases are made from New Melones (CDFG 1998?). A new water temperature model is currently being developed to address this problem.

3.3 GEOMORPHIC PROCESSES AND GRAVEL MINING:

3.3.1 Historical Flows:

The USGS gage (# 11302500) records at Oakdale between 1895 and 1899 provide the best available representation of flows prior to the construction of reservoirs in the watershed (Kondolf 2001). During 1896, 1897, and 1899, the hydrograph can be characterized by (1) flashy winter storms that increased flows up to 14,000 cfs in January and February; (2) snowmelt that provided consistently high flows between 2,000 and 13,000 cfs from March to June, (3) small runoff events between late-September and December, and (4) minimum base flows of 50 to 180 cfs from mid-July through October (Appendix 1). During 1898, which was the driest year between 1895 and 1899, snowmelt flows ranged between 500 to 4,000 cfs flows and the minimum base flow was 27 cfs (Appendix 1).

During the pre-reservoir period, the prolonged period of high flows from snowmelt between March and June corresponds exactly with the time when adult spring-run Chinook salmon and adult stream-maturing (summer-run) steelhead migrated upstream to holding habitat in the upper watershed. Adult ocean-maturing (winter-run) steelhead would have migrated upstream to spawn in the mid- to lower basin during the flashy fall and winter storms. Adult fall-run Chinook salmon probably began their upstream migration in response to small storm events that produced runoff of 50 to 760 cfs between 1895 and 1899 in late-September and October. The runoff from these small storms probably was an important cue for the adult salmon because it provides the scent of their natal stream, which they rely on for navigation once they enter the Delta (Mesick 2001c). Most of the juvenile salmon probably migrated downstream during the high flows during either the winter storms as fry or during the spring snowmelt period as smolts. Most juvenile steelhead would have reared in the Stanislaus River for two years before migrating downstream as 200-mm long smolts during the spring snowmelt period.

3.3.2 Bed Mobility Flow Estimates:

Kondolf and others (2001) conducted a crude bed mobility flow evaluation at five Knights Ferry Gravel Replenishment sites between Goodwin Dam and Oakdale where gravel had been added in late summer 1999. They estimated that flows around 5,000 to 8,000 cfs are necessary to mobilize the median size of the gravel (D50) placed at these sites. They also concluded that higher flows would be needed to mobilize bars to prevent further encroachment of riparian vegetation in the active channel. Before construction of New Melones Dam, a bed mobilizing flow of 5,000 to 8,000 cfs was equivalent to a 1.5 to 1.8 year return interval flow. After the construction of New Melones Dam, 5,000 cfs is approximately a 5-year flow and 8,000 cfs exceeds all flows within the twenty-one year study period.

3.3.3 Sediment Budget:

Kondolf and others (2001) roughly estimate that a minimum of 1,031,800 cubic-yards of gravel were extracted from the active channel and an additional 5,292,500 cubic-yards of gravel were extracted from the floodplain between Goodwin Dam and Oakdale from 1939 to 1999 based on a reconnaissance-level assessment. The total amount of gravel extracted is estimated to be 600% of the amount naturally supplied from the watershed, which is about 1,033,900 cubic-yards. The amount of sand and gravel produced in the unregulated tributaries below Goodwin Dam was estimated to almost two orders of magnitude smaller than the volume extracted. Furthermore, the tributaries below Goodwin dam probably produce a small amount of gravel-sized sediment (Kondolf and others 2001). Kondolf and others (2001) estimated that if mining were to cease today and the natural annual sediment supply was restored, it would take 300 to 400 years to make up for the losses from extraction over the last 50 years.

3.3.4 Geomorphic Changes Due to New Melones Dam:

A study of aerial photographs and field observation by Kondolf et al (2001) indicate that the Stanislaus River has changed from a dynamic river system, characterized by depositional and scour features, to a relatively static and entrenched system. Changes since the construction of New Melones Dam include: (1) large scale vegetation encroachment in the active channel, primarily by willow and blackberry; (2) reduced reproduction of cottonwoods; and (3) substantial encroachment by urban and agricultural development, particularly orchards, in floodplain areas, thereby altering the natural river channel-floodplain connection. Kondolf and others (2001) also speculate that the dam reduced channel diversity through loss of alternating bar sequences and that the active channel has become incised. A comparison of field measurements between 1996 and 1999 suggest that the channel widened from 2.3 to 13.4 feet at five different riffles between Two-Mile Bar and Oakdale during prolonged releases in 1997 and 1998 (Schneider 1999, Kondolf and others 2001). However, CMC (2002) speculates that the loss of alternating bar sequences and channel incision was primarily a result of gravel mining in the active channel (see Section 3.3.5). CMC agrees with Kondolf and others (2001) that encroachment of the riparian vegetation and reduced gravel recruitment has led to the coarsening of the bed material, particularly within spawning habitat in the unmined reaches between Goodwin Dam and Honolulu Bar.

3.3.5 In-River Gravel Mining:

Drag lines were used to dredge the gravel and the spawning habitat from several reaches of the active riverbed primarily during the 1940s until about 1980 (P. Frymire, personal communication, see "Notes"). The dredged channels are now either large instream pits or long, uniform ditches that provide almost no habitat for salmonids. CDFG maps of the spawning riffles in 1972 show the locations of dredger tailings and "old drag lines" adjacent to the mined reaches (CMC 2002c). The following table presents the estimated amount of habitat that was mined in different reaches of the lower Stanislaus River based on an evaluation of the 1972 CDFG riffle maps and spawning surveys in 1994 and 1995 by CMC (2002c).

Reach	Percentage Mined	Spawning Riffles/Mile in 1972
Upper Goodwin Canyon, Rivermile 58.5 to 56.0	0.04%	3.6
Knights Ferry, Rivermile 54.7 to 53.5	0.0%	7.5
Lovers Leap, Rivermile 53.5 to 51.6	97.0%	2.6
Below Willms Pond, Rivermile 51.6 to 51.1	0.0%	12.0
Horseshoe Road, Rivermile 51.1 to 49.75	97.5%	2.2
Honolulu Bar, Rivermile 49.75 to 48.5	0.0%	7.2
Above Orange Blossom, Rivermile 58.5 to 47.4	98.2%	0.9
Below Orange Blossom, Rivermile 47.4 to 44.9	0.0%	6.8
Total: 13.15 miles	39.3%	--

Small instream mine pits that occur in the primary salmonid spawning areas include one just upstream of Two-Mile Bar at rivermile 56.9, two adjacent pits near rivermile 53.5, Willm's Pond at rivermile 51.8, and the Button Bush Pond at rivermile 48.2. There is a large, approximately one-mile long pit at rivermile 39.4 that is called the Oakdale Recreation Pond. Captured mine pits trap bedload sediment, store large volumes of sand and silt, and pass sediment-starved water downstream where it typically erodes the channel bed and banks to regain its sediment load (Kondolf and others 2001). At the upstream and downstream ends of the pit, the over-steepened bed is an unstable knickpoint, which causes bed erosion such that the pit elongates in both an upstream and downstream direction. On the Stanislaus River, incision has been limited due to the reduction in channel forming flows since the construction of New Melones Dam.

Dredged channels and pits also reduce flow turbulance and thereby potentially reduce dissolved oxygen concentrations and provide habitat for fish that prey on juvenile salmonids. Reduced dissolved oxygen may contribute to mortality of juvenile and adult salmonids when water temperatures are unsuitably warm in late spring and early fall.

Concentrations of predator species in slow, flowing ditches that lack cover may also result in high rates of juvenile mortality.

3.4 FLOODPLAIN CONVERSION FOR AGRICULTURAL USES:

Typical riparian vegetation along the lower Stanislaus River consists of black cottonwood (Populus trichocarpa), California sycamore (Platanus racemosa), several species of willow (Salix spp.), alder (Alanus spp.) and oak (Quercus spp.), with an understory of California wild grape (Vitis californica), blackberry (Rubus vitifolius), elderberry (Sambucus glauca), and a variety of grasses (CDFG 1972). No analyses have been conducted to assess the amount of riparian habitat along the lower Stanislaus River that has been converted for agricultural use or commercial gravel mining. The Department of Fish and Game conducted analyses of aerial photographs taken in 1958 and 1965 that indicated that there were approximately 3,300 acres of riparian habitat between the Knights Ferry Bridge and the San Joaquin River in 1958, but only 2,550 acres in 1965 as a result of conversion for agricultural uses and commercial gravel mining (CDFG 1972). The amount of riparian habitat appears to have stabilized since 1965 based on a third analysis conducted by the U.S. Fish and Wildlife Service with 1994 aerial photos (USFWS 1995). The USFWS analysis indicates that there were approximately 2,590 acres of riparian and wetland habitat in this reach (see table below). They also estimated that there were approximately 4,155 acres of agricultural land, 725 acres of land disturbed primarily for commercial gravel mining, and 823 acres of land converted for urban use within a 1,500 foot wide corridor of riparian and upland habitats in this reach (USFWS 1995). Moreover, the presence of riparian habitat does not imply that connectivity exists between the floodplain and the active channel under the current flow regime; instead, groundwater may sustain some species of riparian vegetation without flooding. Although the USFWS study did not distinguish between riparian/floodplain habitat and upland habitat and so the amount of riparian habitat converted for agricultural and mining use cannot be estimated with this data, the USFWS habitat maps clearly indicate that much of the riparian habitat of the lower Stanislaus River has been converted into other uses (USFWS 1995).

The Foothill Reach began at the covered bridge in Knights Ferry and ended at the Orange Blossom Bridge. The Valley Reach began at the Orange Blossom Bridge and ended at the confluence with the San Joaquin River.

3.5 DOWNSTREAM CONDITIONS:

Although beyond the scope of this restoration plan, the survival of anadromous fish of the Stanislaus River is highly dependent on conditions in the mainstem San Joaquin River, San Joaquin Delta, San Francisco Bay estuary, and ocean.

3.5.1 Delta Reclamation and the Deep-Water Ship Channel:

Prior to 1850, the Sacramento-San Joaquin Delta, an area of nearly 750,000 acres, was mostly a tidal marsh that consisted of a network of sloughs and channels during low flows and a large inland lake during flooding. The development of the Delta into farmland began in 1850 when the Swamp Land Act conveyed ownership of all swamp and marshes from the federal government to the State. Initial reclamation consisted of the construction of levees with peat soils on Rough and Ready Island and Roberts Island. These initial levees failed and in the 1870s steam-powered dredges were used to excavate alluvial soils to construct much larger levees. By the 1930s, reclamation was considered complete and the number of operating dredges declined greatly. However, due to continued subsidence of the peat soils, the Army Corps of Engineers continually adds material to maintain the levees, many of which range between 15 and 25 feet high.

The Port of Stockton and the deepwater ship channel in the San Joaquin Delta were completed in 1933. Activity at the Port of Stockton increased greatly in 1942 with the construction of military ships, mine sweepers, and landing craft. Shortly thereafter, large passenger cruise ships began navigating through the Delta. Currently the river is dredged to a depth of 35 feet to allow passage of deep draft ships; whereas upstream of the ship channel, depths range between 8 and 12 feet.

The Port of Stockton has recently contracted with the U.S. Army Corps of Engineers (ACOE) to study the feasibility of deepening the deep-water ship channel between the port and Pittsburg (The Sacramento Bee, July 18, 2002). The first phase of the study will analyze the effects on water quality and the economics of deepening the 25-mile channel.

3.5.2 Water Quality in the Deep-Water Ship Channel:

Dissolved oxygen (D.O.) concentrations are low in the deep-water ship channel during summer and early fall months partly (if not primarily) as a result of the decomposition of algal biomass that is produced in the comparatively shallow, nutrient-rich water upstream of Mossdale and subsequently transported into the much deeper waters of the ship channel (McCarty 1969; Van Nieuwenhuyse, personal communication). The algae, mostly diatoms, are not adapted to deep-water conditions and quickly settle out and decompose on the streambed. Simulations performed using the City of Stockton's D.O. model (Schanz and Chen 1993) indicate that increasing flow at Vernalis with the head of Old River barrier closed generally improves D.O. conditions at Stockton during most months. But in October, warm temperatures and the D.O. demand exerted by ammonia from the Stockton wastewater plant, the rotting algal biomass, and other organic matter usually keep D.O. levels well below the 6 mg/l standard.

The chlorophyll levels at Vernalis are literally among the highest ever recorded for streams worldwide and much of this production may be fueled by feedlot operations in the catchment. On the other hand, it is possible that the nutrient loading responsible for the high algal production stems from much more diffuse processes, such as tile drainage from row crops or orchards. An EPA-style TMDL (total maximum daily load) analysis for nutrients (especially phosphorus) for the San Joaquin catchment would be the first step toward resolving these issues (Lee and Jones-Lee 2001).

The Stockton D.O. model does not yet explicitly include algae, however, so its predictions about the effects of increased flow should be viewed with healthy skepticism. It is conceivable that under some circumstances sending more Vernalis water to the ship channel could make matters worse by increasing its organic matter loading rate. Ideally, the continuous monitoring stations upstream of the ship channel would be equipped with fluorometers calibrated to measure chlorophyll concentration (an indirect measure of algal biomass). Such a system would alert managers when algal biomass levels at Vernalis or further upstream are extremely high and give them time to take appropriate action.

Under most circumstances, the loading of algal biomass produced naturally in the San Joaquin river upstream is probably a much more serious problem for D.O. in the ship channel than organic matter loading from the Stockton wastewater treatment ponds. The loading of dissociated ammonium from the wastewater facility, however, may pose a potential toxicity problem. When algae are abundant and D.O. upstream becomes supersaturated (due to photosynthesis), pH levels also increase. High pH and high ammonium concentration lead to higher levels of undissociated ammonia, which is toxic to fish and aquatic invertebrates. It is possible that the salmon are responding to this toxicity rather than to low D.O.

4.1 INTRODUCTION:

The following conceptual models are summaries of the available evidence and the "best guesses" of the members of the Stanislaus Fish Group as to how habitat degradation and other limiting factors have caused the decline of Chinook salmon and steelhead in the Stanislaus River. The conceptual model is the centerpiece of this restoration plan because it identifies important data gaps in our understanding of the ecological processes that led to the fishes' decline in the lower Stanislaus River. It also highlights the obvious problems that if corrected should result in a measureable increase in the abundance of the target species.

The model helps identify data gaps in two ways. First, it provides a summary of all the evidence regarding the causes that led to the fishes' decline. Second, it includes all the alternative theories presented by various stakeholders of what caused the decline of the fish populations. By viewing the model as a set of interlinked hypotheses, it provides the guidance needed to design the monitoring, focused research, and pilot restoration actions to resolve uncertainties to the satisfaction of all stakeholders and to determine the most effective way to restore and manage the river. Important data gaps identified within the conceptual model are categorized as high priority.

The model is also useful for identifying actions for which there is sufficient evidence that they should provide measureable increases in fish abundance. Even when there is sufficient evidence that a problem should be corrected, most projects have been designed with an adaptive management approach to help refine our restoration methods. These projects are also recommended as a high priority for funding and implementation.

Conceptual models were developed for the life stages for each of the three target species in the lower Stanislaus River: spring-run Chinook salmon (Section 4.2), fall-run Chinook salmon (Section 4.3), and steelhead (Section 4.4).

4.2 SPRING-RUN CHINOOK SALMON:

Although spring-run salmon probably declined in response to the hydraulic mining in the Stanislaus River watershed and the dredging of the Delta during the late 1880s, it is highly likely that their populations have not rebounded because the upstream dams block the migration of adult fish into the upper watershed. Migration into the upper watershed during high spring flows may have been critical for spring-run because it separated them from the fall-run salmon that were confined to the lower watershed by low fall flows. Although the habitat downstream of Goodwin Dam should provide suitable habitat for spring-run due to the year-round hypolimnetic releases of relatively cold water from New Melones Reservoir, competition for spawning habitat and genetic contamination with fall-run are believed to prevent the recovery of spring-run confined to the lower Stanislaus River.

Other factors that depress spring-run Chinook salmon populations are probably similar to those that impact fall-run Chinook salmon and are discussed in Section 4.3.

4.2.1 Adult Upstream Migration:

It is likely that flows and water temperatures are adequate for adult spring-run to complete their migration into the Stanislaus River between mid-February and mid-May. Hallock and others (1970) reported that tagged fall-run adults migrating in the San Joaquin River usually moved past Stockton when water temperatures dropped to less than 66 oF. Water temperatures in the San Joaquin River near Vernalis were usually less than 65 oF prior to mid-April when Vernalis flows exceeded about 1,500 cfs between 1962 and 1994 (Mesick 2001a). Water temperatures should also be less than 65 degrees between late-April and mid-May (extended to June 1 in wet years) due to thirty-day pulse flow releases of about 1,500 cfs from each San Joaquin River tributary that began in 1993 to enhance the survival of juvenile fall-run salmon migrating through the Delta.

However after the pulse flows cease in mid-May, the migration of late-arriving adults may be delayed or blocked due to unsuitably warm water temperatures in the lower San Joaquin River. Water temperatures at Vernalis frequently exceeded 65 oF in late May regardless of the streamflow (up to about 30,000 cfs) at Vernalis and presumably this would block the passage of adult salmon in the Delta near Stockton where D.O. and water quality are poor (Mesick 2001a). On the other hand, migrations may be possible intermittently when water temperatures are below 65 oF for several days at a time presumably due to Delta breezes and reduced air temperatures (Mesick 2001a). If the San Joaquin River basin populations of spring-run salmon had similar migration patterns to those in the Sacramento River basin, then up to one-third of the spring-run population in the Stanislaus River would have migrated through the Delta after mid-May. The extent of this impact depends on (1) whether adult spring-run are able to complete their migration into the Stanislaus River during the brief periods when water temperatures are below 65 degrees in the San Joaquin River after mid-May; and (2) whether delays of migrating fish in the Delta due to warm temperatures would harm the unfertilized gametes in the adult fish. These questions cannot be answered at this time.

Another concern is that excessive exports in the Delta at the Central Valley Project (CVP) and State Water Project (SWP) may increase adult straying rates. The percentage of coded-wire-tagged San Joaquin fall-run Chinook salmon that strayed to the Sacramento River basin or one of the eastside streams increased up to about 20% whenever more than 400% of the San Joaquin River flow at Vernalis was exported from 1979 to 1996 (Mesick 2001b). A 10-day pulse flow released from the San Joaquin River tributaries that resulted in export rates less than 3% in mid-October, which was the peak migration period in the Delta, was sufficient to minimize straying. It is reasonable to assume that if exports exceed 400% of San Joaquin River flows during the upstream migration period, then migrating adults might stray to the Sacramento basin or they could be delayed until the spring pulse flow. Straying of adult spring-run to the Sacramento basin jeopardizes the San Joaquin basin populations by reducing the number of San Joaquin basin juveniles produced.

4.2.2 Adult Holding Habitat:

CDFG (1998) describes spring-run holding habitat as consisting of (1) deep pools, (2) adequate cover, such as bubble curtains created by flowing water, (3) proximity to spawning gravel, and (4) adequate water temperatures and dissolved oxygen concentrations. The high recreational use of the Stanislaus River by rafters probably increases the importance of cover or particularly deep pools for holding habitat. Although the long deep pools in Goodwin Canyon do not contain spawning gravel, a few spring-run were observed there in summer 2000 (Fisheries Foundation 2002). Holding habitat currently exists at numerous sites in Goodwin Canyon, six of the Knights Ferry Gravel Replenishment sites near Lovers Leap (riffles R13, R14, R14A, R15, R19, and R19A), and four riffles adjacent to deep mine pits near Frymire Ranch (RM 53.4), "Willms Pond" (RM 51.8), and Button Bush Park (RM 48).

It is likely that summer water temperatures were suitable for holding adult salmon in recent years, except perhaps 1991. Mean daily flows at the Orange Blossom Bridge (DWR gage) were usually greater than 200 cfs from June through September between 1991 and 2001; however, flows were near 110 cfs for about 45 days during summer 1991. The US Bureau of Reclamation Stanislaus River Basin Water Temperature Model (Rowell 1993) predicts that at a base flow of 200 cfs, weekly mean water temperatures at the Orange Blossom Bridge would range between 59.5 and 66.8 oF from June through September when the temperature of releases from Goodwin dam were moderate. Rowell (1993) did not model temperatures for base flows less than 200 cfs. USGS measurements indicate that hourly water temperatures ranged between 55 and 65 oF at the Orange Blossom Bridge during summer 2001 when flows ranged between 287 and 840 cfs. The Biological Opinion for the USBOR operations for New Melones Reservoir (NMFS 2002) directs that sufficient flows are to be released to maintain water temperatures below 65 degrees (at the Orange Blossom Bridge or below Goodwin Dam?). Overall, it is highly unlikely that either the quality or quantity of adult holding habitat currently limits the spring-run population in the Stanislaus River.

4.2.3 Spawning and Incubation Habitat:

It is likely that fall-run salmon destroy many of the spring-run redds because spring-run spawn first which leaves their redds vulnerable to superimposition by fall-run salmon. Spring-run typically spawn in September and October, whereas fall-run salmon spawn between late-October and December. Redd superimposition by fall-run salmon would probably kill many of the spring-run eggs or entomb spring-run alevins by burying the spring-run redd with silt and sand (CMC 2002b). When fall-run escapement was approximately 8,500 fish in fall 2000, redd superimposition from fall-run salmon completely disturbed 33% of egg pockets and buried another 21% of egg pockets of artificial redds constructed in September and October between Knights Ferry and Willms Pond (CMC 2002b). Redd superimposition rates may also be high when escapement is relatively low as salmon prefer to spawn in loose gravel, as occurs in newly constructed redds in the highly compacted, natural spawning sites in the Stanislaus River. In fall 1996, when escapement was estimated at 168 fish, redd superimposition completely disturbed 24% of the egg pockets of salmon redds marked with pipe piezometers over an eight-day period in mid November (Mesick 2001b). Although redd superimposition by fall-run salmon may destroy 40 to 50% of the spring-run eggs each year, it seems unlikely that this mortality factor alone could prevent the recovery of the spring-run Chinook population in the Stanislaus River.

Another problem for spring-run using the lower river is that fall-run salmon probably interbreed with spring-run fish and interbreeding probably results in genetic contamination that would alter their migratory behavior. There are no behavioral differences that would prevent spring-run and fall-run from interbreeding as fish from each run would be present together in late October when both would be spawning. This may be a substantial problem for the recovery of the spring-run since there would be several fall-run adults that could interbreed with each spring-run adult in late October.

Other factors such as high water temperatures or turbid storm runoff probably do not have a significant impact on incubating spring-run eggs. Surface and intragravel water temperatures were almost always less than 56 degrees during late-October and early-November in 1996 (CMC 1997), 1999, 2000 (CMC 2002a, 2002b) between Goodwin Dam and the Orange Blossom Bridge, whereas egg mortality begins to occur at 58 degrees (CDFG 1998). Moreover, the eggs would have hatched and most would have emerged by mid-January, when intensive turbid storm runoff usually begins in the Stanislaus River.

4.2.4 Juvenile Rearing Habitat:

Although spring-run juveniles are subjected to the same impacts that affect fall-run juveniles, such as in-channel gravel mining, exotic predators, and reductions in flow and floodplain inundation, spring-run juveniles emerge before the fall-run juveniles and so they would have a competitive edge for the best rearing habitat. Therefore, it is unlikely that degraded juvenile rearing habitat has prevented the recovery of the spring-run population.

4.2.5 Juvenile Migration:

Spring-run juveniles would also begin their migrations earlier than the fall-run juveniles when mortality rates are probably at their lowest. Although it is possible that the application of dormant sprays in the lowermost reaches of the Stanislaus River, San Joaquin River, and Delta during the winter could cause substantial mortality of spring-run juveniles, this would primarily affect fry that migrate from the upstream rearing areas during the early winter. However, since spring-run juveniles would be the first to emerge and establish territories in suitable rearing habitat, it is likely that most remain in the upstream areas that are unaffected by the dormant sprays.

4.3 FALL-RUN CHINOOK SALMON:

The fall-run Chinook salmon population in the Stanislaus River is probably impacted by many factors, although mortality rates have not been quantified for any of the factors. One of the most prominent limiting factors appears to be the high rates of mortality for juveniles migrating through dredged channels in the Stanislaus River and Delta, particularly the Stockton deep-water ship channel. The survival of juvenile fish in the deep-water ship channel is highest during flood flows or when a barrier is placed at the head of the Old River that more than doubles the flow in the ship channel. Escapement is also directly correlated with springtime flows when each brood migrates downstream as smolts. However, the cause of the mortality in the ship channel has not been studied. It is possible that mortality results from the combined effects of high water temperatures, low dissolved oxygen concentrations, ammonia toxicity, and predation.

Dredging for gravel and gold in much of the Stanislaus River's streambed primarily during the 1940s has substantially limited the availability of spawning and rearing habitat. It is also possible that the dredged areas store fine sediments that are transported to spawning and rearing habitats during high flows. The dredged areas also contain an abundance of large predatory fish although there is uncertainty as to whether predation is a substantial source of mortality of juvenile salmon.

Spawning and rearing habitat in the lower Stanislaus River are further degraded by highly regulated flows and the diking of floodplains for agriculture. The Stanislaus River's streamflow is highly regulated by over forty dams, with 85% of the total storage contained in New Melones Reservoir, which began to fill in 1981 (Kondolf and others 2001). The reservoirs have greatly reduced the amplitude and frequency of flood flows and together with the dikes, very little of the historical floodplains are inundated. Without inundation, the floodplains cannot provide terrestrial food for juvenile salmon or organic matter that helps produce more food within the river. Moreover, the lack of peak flood flows allows encroachment of riparian vegetation, which along with the dikes tend to confine flood flows to the river channel. This in turn accelerates the rate that gravel is scoured from spawning and rearing habitat. With high rates of scour, spawning and rearing habitat tends to erode away and the river tends to widen because the upstream reservoirs block gravel recruitment from the upper watershed (Kondolf and others 2001).

Another problem that resulted from the construction of New Melones Reservoir is that housing developments began to rapidly encroach on the floodplain. Housing construction near the river has led to high rates of sedimentation in the upstream areas near the Orange Blossom Bridge. The sedimentation may result in mortality of incubating Chinook salmon eggs and it probably reduces the production of aquatic invertebrates that provide food for juvenile salmon.

Water diversions for urban and agricultural use in all three San Joaquin River tributaries reduce flows and potentially result in unsuitably high water temperatures during the spring and fall for juveniles and adults rearing and migrating in the lower San Joaquin River and Delta. Currently, flow releases from Friant Dam on the mainstem San Joaquin River do not reach the confluence with the Merced River except during wet years. Moreover, base flows on the Tuolumne and Merced rivers during dry and normal years are low compared to those on the Stanislaus River. In addition, agricultural return flows are particularly high in the mainstem San Joaquin River, primarily from Mud and Salt sloughs, and the concentration of contaminants and warm temperatures are probably detrimental to rearing juveniles.

The federal and state pumping facilities in the Delta have impacted juvenile and adult salmon since pumping began at the federally operated Central Valley Project in 1951. Pumping up to a combined current maximum of 11,000 cfs for the federal and state pumping facilities during the spring diverts water into the Old River from the mainstem San Joaquin River. Studies suggest that high rates of pumping reduce juvenile survival in both the deep-water ship channel and in the Old River, except during flooding (Mesick 2001a). Recently, smolts migrating in the Delta have been protected between mid-April and mid-May with a barrier at the head of the Old River, a reduction in pumping rates, and pulse flow releases from all three tributaries. As a result of these protections, juvenile survival in the Delta has more than doubled to between 30% and 60% based on studies of tagged smolts that were reared in the Merced River Fish Facility and released at Mossdale and Dos Reis (Mesick 2001a, SJRGA 2002). However, fry that migrate into the mainstem San Joaquin River are usually subjected to the maximum pumping rates without the protection of the barrier at the head of the Old River. Moreover, adult salmon migrating upstream to spawn in the San Joaquin tributaries can stray into the Sacramento basin if pumping rates exceed 400% of San Joaquin River flows in mid-October (Mesick 2001c). Pulse flows have been released from all three tributaries since 1994 to minimize straying; however, DWR's Interim South Delta Program may increase fall pumping rates in the near future and pulse flows were relatively low in fall 2002.

Overall, these impacts affect every aspect of the salmon's life history:

• The spawners are crowded into a few areas, many of which are highly silted, and both the crowding and siltation results in high rates of egg mortality. Crowding is a consequence of (1) past in-river gravel mining that excavated approximately 40% of the spawning beds in the river, and to a lesser extent the (2) coarsening of the remaining spawning bed gravels due to upstream dams blocking gravel recruitment and abnormally high rates of scour caused by vegetation encroachment and dike construction that isolates floodplain habitat from the active river, and (3) siltation of the remaining spawning areas downstream of the Orange Blossom Bridge;
  
• Some fry prematurely migrate downstream because much of the rearing habitat was dredged and their survival rates are relatively low in the San Joaquin River and Delta;
  
• Low flows, warm temperatures, ammonia toxicity, and low dissolved oxygen concentrations, particularly in the San Joaquin River and Delta, increase both predator activity and physiological stress for migrating juveniles; and
  
• High Delta export rates can cause up to about 20% of adult Stanislaus River fish to stray into the Sacramento basin and entrain juvenile salmon in the spring.
  
• There are insufficient data to quantify the impacts of

a) Dikes and encroached vegetation that isolate floodplain habitat from the river on spawning habitat suitability, food availability for juvenile salmonids, juvenile refuge habitat during flooding;
b) Predation, particularly in mined channels;
c) Disease;
d) Unscreened diversions downstream of Oakdale, the San Joaquin River, and Delta;
e) Contaminants in agricultural and urban runoff;
f) High water temperatures during late spring, summer, and early fall; and
g) Reduced dissolved oxygen concentrations in dredged channels.

4.3.1 Adult Upstream Migration:

Poor water quality in the deep-water ship channel near Stockton and excessive exports at the State Water Project and Central Valley Project at Tracy can either delay the upstream migration of adults or cause them to stray to the Sacramento River basin. Since 1993, 10-day pulse flows from the three San Joaquin River tributaries in mid-October have probably minimized these problems.

Delayed Adult Migration:

Hallock and others (1970) showed that radio-tagged adult chinook salmon delayed their migration at Stockton whenever dissolved oxygen (D.O.) concentrations were less than 5 mg/l in October during the 1960s (and possibly water temperatures that exceeded about 65 oF) and there are concerns that if adult salmon are delayed in the Delta that egg and milt viability may be reduced and the harvest of adults may be increased before spawning occurs. They reported that D.O. levels usually increased to suitable levels by November when upstream migrations resumed.

D.O. concentrations near Stockton in October and November were greater than 5 mg/l from 1983, when DWR began monitoring, to 1990, but were substantially lower than 5 mg/l for most of October in 1991 and 1992. The Head of the Old River Barrier was installed in fall 1992, but it did not correct the problem. In 1993, D.O. levels were low until about 10 October and it is likely that pulse flows that raised Vernalis flows to about 4,000 cfs on 7 October were responsible for increasing D.O. levels at Stockton. Similarly in 1994, D.O. levels were low until 15 October when pulse flows raised Vernalis flows to about 2,000 cfs. In 1995, D.O. levels were near 5 mg/l in mid to late September until Vernalis flows increased from about 3,000 cfs to 6,000 cfs through mid October. Low D.O. levels also occurred in 1996 until 12 October when pulse flow releases increased Vernalis flows from 2,000 to about 3,000 cfs.

Adult Straying:

Delta export rates at the State Water Project and Central Valley Project were increased to near maximum (about 9,600 cfs) in fall 1996 and in subsequent years to "make-up" for reduced pumping rates during the spring outmigration period to improve salmon smolt survival. The adult fall-run salmon are migrating upstream through the Delta primarily in October typically when San Joaquin River flows measured at Vernalis are low (Mesick 2001c). It is likely that when exports are high relative to San Joaquin River flows, little if any San Joaquin River water reaches the San Francisco Bay where it may be needed to help guide the salmon back to their natal stream. An analysis by Mesick (2001c) of the recovered adult salmon with coded-wire-tags (CWT) that had been reared at the Merced River Fish Facility and released in one of the San Joaquin tributaries suggests straying occurred when the ratio of exports to flows was high. The analysis, which included an adjustment to the estimated number of fish examined for CWTs in some rivers, indicates that during mid October from 1987 through 1989 when export rates exceeded 400% of Vernalis flows, straying rates ranged between 11% and 17%. In contrast, straying rates were estimated to be less than 3% when Delta export rates were less than about 300% of San Joaquin River flow at Vernalis during mid-October. Since 1993, pulse flow releases from the San Joaquin tributaries for 8 to 10 days in mid-October appear to have kept straying rates below 2%.

Delta Migration Barriers:

In the South Delta, rock barriers are installed to maintain hydraulic head for small pump diversions and these barriers are impassible for adult salmonids. Hallock and others (1970) found that when the head of Old River barrier was installed in fall 1964, adult salmon migrated through the mainstem San Joaquin River. However, when the barrier was not installed in fall 1965 through 1967, some of the salmon migrated through the South Delta. Their study suggests the rock barriers block the flow of water that attracted migrating adults and so few, if any, adults would be expected to migrate into channels where rock barriers have been installed.

4.3.2 Spawning and Incubation Habitat:

Although the historical spawning reach for fall-run Chinook salmon has been described as a ten-mile reach that extended from the marshlands above Oakdale (possibly Kerr Park at rivermile 43.5) to Knights Ferry by Clark (1929), spawning typically occurs at about 120 natural riffles between Goodwin Dam and Jacob Meyers Park in Riverbank with only a slight decline in redd density in a downstream direction (CMC 2001; Mesick 2001b). However, from fall 1998 to 2000, redd densities declined substantially in a downstream direction with few fish spawning near Oakdale (CMC 2001, 2002a, 2002b).

Surveys in 1994 and 1995 indicated that approximately 73% of the redds occurred in the uppermost 30-foot sections of the riffles although the habitat in the downstream sections of the riffles appeared to have similar water depths, velocities, and gravel sizes compared to the highly used upstream sections (Mesick 2001b). Detailed measurements at 12 riffles indicated that most redds were constructed where the streambed was rising in a downstream direction (e.g., tail of a pool); intragravel dissolved oxygen concentrations were usually high at these areas although downwelling could not be detected with a manometer (Mesick 2001b). This suggests that adult Chinook salmon require cover as provided by the pools immediately upstream of their spawning habitat. Apparently, gravel more than about 30 feet from pool habitat or other forms of cover are not used by spawning adults.

Although several studies have indicated that there are relatively high concentrations of sand and silt in the spawning riffles in the Stanislaus River (DWR 1994; Mesick 2001b, CMC 2001), Chinook salmon are able to effectively remove most of the fines during the construction of their redds (CMC 2002b). However, the fines pose a problem during redd superimposition when fish construct their redd immediately upstream of a pre-existing redd. During the construction the new redd, the superimposed redd becomes covered with fines which can entomb the alevins (CMC 2002b) and possibly reduce downwelling of oxygen-rich surface flows into the egg pocket.

Redd superimposition may be a substantial problem for salmon in the Stanislaus River. High rates of redd superimposition have been observed in the Stanislaus River since 1994 regardless of the number of spawners, partially because they tend to crowd themselves into a relatively few sites in the upstream areas where much of the spawning habitat has been excavated. Approximately 57% of the spawning habitat has been mined for gravel and 33% of the riffles between Goodwin Dam and the Orange Blossom Bridge have become somewhat armored due to the lack of gravel recruitment (Mesick 2002). Although gravel has been added to several sites in Goodwin Canyon since 1997 by the Department of Fish and Game and to 18 sites between Two-Mile Bar and Oakdale in 1998 (CMC 2002a), the amount of gravel added to the river is less than 1% of the estimated 1,031,800 cubic-yards of gravel that were excavated from the active channel between 1939 and 1999 (Kondolf and others 2001).

Most of the riffles that remain in the unmined areas are either somewhat armored, such that large rocks, which are difficult for the adults to move, cover the surface layer of the streambed, or they are cemented because the loose gravel has been gradually washed away by high flows. It is likely that adult salmon tend to superimpose their redds on top of existing redds in the Stanislaus River simply because it is easy to dig in a new redd compared to nearby areas that are either covered with large rocks or consist of cemented gravel. Redd superimposition would have the greatest impact on redds constructed early in the season (e.g., late October and early November) because they would be the most vulnerable to late-arriving fish. Based on fall 2000 studies with artificial redds (CMC 2002b), approximately 33% of the early redds would be completely destroyed during redd superimposition and another 21% of the early redds would be buried by the fines cleaned from the superimposing redd that could entomb many of the alevins and reduce the downwelling of oxygen-rich surface water into the egg pocket. Mortality rates due to entombment in superimposed redds have not been quantified.

Another likely problem is that intensive rainstorms, which typically occur in January and February, result in turbid storm runoff. When runoff is high from intensive rainstorms, flows become turbid at Knights Ferry and turbidity increases in a downstream direction, particularly starting near the housing developments just upstream of the Orange Blossom Bridge. After an intensive rainstorm on 25 January 2000, there was a thick blanket of clay-sized silt covering the riffles at Knights Ferry and the downstream areas, particularly those below the Orange Blossom Bridge (CMC 2002a). This amount of silt had not been observed following intensive storms in January 1996 and so the new housing developments are the most likely cause. It is possible that the recent heavy siltation from the housing developments caused a shift in the distribution of spawners to the upstream areas beginning in fall 1998 (CMC 2001, 2002a, 2002b). However, spring 1999 pulse flows flushed most of the silt from the spawning beds (CMC 2002a) and so there is no obvious mechanism that would have caused the fish to shift their spawning distribution. Although agriculture probably contributes much less turbidity than the new housing developments, turbidity increases in response to erosion of unpaved roads and the trenching of pastures to drain standing water that accumulates during intensive rainstorms. Bank erosion occurs at isolated locations and does not appear to be a substantial problem between Goodwin Dam and Oakdale.

Turbid storm runoff in January and February probably impacts redds constructed after mid-November that would still contain incubating eggs during the storms. Even though salmon can clean the gravel and create highly permeable intragravel conditions during redd construction (CMC 2002b), suspended clay-sized particles in turbid storm runoff can penetrate the egg pockets and coat the surface of the eggs. Coating the surface of the eggs with silt probably reduces the ability of the egg to absorb oxygen (CMC 2002a). Eggs incubating in clean laboratory conditions can survive at dissolved oxygen concentrations as low as about 2 mg/l whereas those incubated in silty, natural environments require up to 8 mg/l dissolved oxygen concentrations for survival. Eggs incubated under low oxygen concentrations also tend to produce stunted alevins that may be too weak to emerge through the sand layers covering the egg pocket or compete with healthy alevins for food after emergence.

Another problem with turbid storm runoff is that fine sediment intrusion can seal the sand layer covering the egg pocket thereby reducing the downwelling of oxygen-rich surface water into the egg pocket and simultaneously increasing the flow of oxygen-poor groundwater into the egg pocket. In February 1996, intragravel dissolved oxygen concentrations declined by 25% to 75% in several artificial redds after four intensive rainstorms in January increased mean daily flows by an average of 200 to 500 cfs for several days after each storm (Mesick 2001b). Again, this problem would affect primarily incubating eggs in redds constructed after mid-November, whereas alevins, which have gills, would probably survive low dissolved oxygen concentrations.

Although studies have not been conducted to quantify the effects of redd superimposition and sedimentation on Chinook salmon egg survival in the Stanislaus River, the Stanislaus River can support the progeny of only about 1,250 adult female salmon based on a stock-recruitment analysis for the Stanislaus River salmon population from 1946 to 1998 (Mesick 2001a).

Gravel Mining Impacts:

The coarsening of substrate size in spawning beds in the lower Stanislaus River has resulted from the combined impacts of gravel mining, upstream dams that block recruitment of spawning-sized gravel and increased rates of scour due to the isolation of floodplain lands from the river channel. Instream gravel and gold mining, which peaked during the early 1940s and ceased prior to 1980, completely excavated approximately 44% of the spawning habitat from the 10-mile reach between Goodwin Dam and the Orange Blossom Bridge (CMC 2002c), where most Chinook salmon and steelhead spawn in the lower Stanislaus River (CMC 2001, Mesick 2001b). The upstream dams that blocked the coarse sediment supply and the isolation of floodplain habitat from the active river with dikes worsened the problem as some of the riffles in the unmined reaches have became armored and smaller as the gravel gradually eroded away (CMC 2002c). Furthermore, there is evidence that the blockage of gravel recruitment and the isolation of floodplain habitat is causing channel widening during periods of high flows (Kondolf and others 2001). However, there are a few sections of the river between Goodwin Dam and the Orange Blossom Bridge that were not mined where gravel is mobilized from riffle to riffle and most of the habitat is still highly suitable for spawning (CMC 2002c). The presence of these highly functional sections of river suggests that lack of spawning-sized gravel in the lower Stanislaus River is primarily due to past gravel mining operations.

Loss of Floodplain Habitat:

During flooding when floodplain habitats are overtopped, fine sediments are deposited on the floodplain's surface, which helps remove fines from in-river spawning habitat (Kondolf and others 2001). Diking of floodplain habitat from the active channel prevents the separation of fine sediments from spawning-size gravel during periods of bed mobilization. Gravel deposited at spawning beds in the lower Stanislaus River near the Horseshoe Road Park and Oakdale during the spring 1997 high flows appeared to have high concentrations of fine sediments (Mesick 2001b). Intragravel dissolved oxygen concentrations were suitable at the Horseshoe Road Park site (Riffle R27) but low for incubating salmonid eggs at the Oakdale site (Riffle R78) during fall 1997 (Mesick 2001b).

4.3.3 Juvenile Rearing Habitat:

Soon after emergence, concentrations of fry were observed in slow-water, margin habitats of eight study sites from about a mile below Goodwin Dam (rivermile 57.5) downstream to Oakdale (rivermile 40) in 2000 and 2001 (Fisheries Foundation 2002). Fry densities were highest between Knights Ferry and the Honolulu Bar sites. As they grew through the spring, juvenile salmon were evenly distributed between Two-Mile Bar and Oakdale, where they were relatively abundant in fast-water, riffle habitat, particularly at the Knights Ferry Gravel Replenishment Project (KFGRP) restoration sites. Although the juvenile salmon utilized fast-water areas without bankside vegetation, densities were highest where bankside vegetation provided cover adjacent to fast-water habitat. During the summer through mid September, large juveniles were observed downstream to the Orange Blossom Bridge site. From September 27 to November 19, 2001, few juveniles were observed in the river although water temperatures never exceeded 65 oF at the Orange Blossom Bridge during summer 2001 (CDEC web site). The Fishery Foundation surveys did not address the suitability of the habitat downstream of Oakdale for rearing juveniles.

It is likely that excavation of riffle habitat for gravel mining has substantially degraded juvenile rearing habitat. The snorkel surveys conducted by the Fisheries Foundation (2002) indicate that juvenile densities were highest at the KFGRP sites where gravel berms were constructed in the shape of the tails of pools. This highly porous gravel probably provided shallow habitat that was relatively free of predators and contained an abundance of aquatic invertebrates for food. In contrast, the mined channels have abnormally high densities of large Sacramento pikeminnow (Ptychocheilus grandis) that feed on newly emerged fry (Walser, personal communication, see "Notes"). However, no studies have quantified the effect of mining on mortality rates or food production and the attraction of juvenile salmon to the KFGRP gravel berms is not an indication of improved survival.

It is also possible that the lack of rearing habitat due to in-river gravel mining between Goodwin Dam and Oakdale causes fry to pre-maturely migrate from the Stanislaus River to the Delta. Survival of fry and larger juveniles in the lower Stanislaus River and San Joaquin Delta is relatively low during dry and normal years (Brandes and McLain 2001), and it is widely believed that most die from a combination of factors including high water temperatures, poor water quality in the deep-water ship channel, predation, contaminants from agricultural runoff, and entrainment in unscreened diversions (Herren and Kawasaki 2001).

Flows and Water Temperatures:

Streamflow releases from Goodwin Dam are probably adequate to provide suitable water depths, velocities (USFWS 1993), and water temperature (USBOR 1993) for juvenile salmon under the 1987 agreement between CDFG and USBOR, except perhaps during extremely dry years when the fishery flow allocation is reduced 69,000 acre-feet under a recent variant to the SWRCB Decision 1422. This is partly true because fishery flows are augmented under the CVPIA (b)(2) program depending on the availability and need for increased flows. Moreover, the 2002 NMFS biological opinion on interim operations of the Central Valley Project (CVP) and State Water Project (SWP) on federally listed threatened Central Valley spring-run chinook salmon and threatened Central Valley steelhead in accordance with section 7 of the Endangered Species Act of 1973 (ESA) includes a non-discretionary measure for the USBOR to maintain water temperatures with flow releases to no more than a mean daily average of 65 oF (between Goodwin Dam and the Orange Blossom Bridge or just below Goodwin Dam?) from June 1 through September 30 to protect over-summering steelhead from thermal stress and from warm water predator species. During a hot spell in early August 2002 when maximum daily air temperatures in Modesto ranged between 99 and 103 oF, flow releases of 200 and 225 cfs kept the mean daily water temperatures at Orange Blossom Bridge at or below 64 oF. The maximum daily water temperature was 66.3 oF during this period.

Suitable water temperatures for juvenile fall-run Chinook salmon in the Central Valley are somewhat in dispute because laboratory tests suggest that Central Valley Chinook salmon are relatively sensitive to high water temperatures compared to Chinook salmon from the Pacific Northwest. For example, juvenile Chinook salmon from the American River suffered chronic sublethal stress at water temperatures above 60 oF (15.6 oC; Rich 1987) and mortality occurred at 77 oF (25 oC) for fish from the Mokelumne River Fish Hatchery after about 100 minutes of exposure (Hanson 1991). In contrast, juvenile spring-run Chinook salmon from British Columbia grew at maximum rates at water temperatures between 66 and 68 oF (19 to 20 oC) when fed to satiation, whereas mortality also occurred at 77 oF (Brett and others 1982).

Dissolved Oxygen:

The excavation of riffle habitat reduces flow turbulence, which probably reduces dissolved oxygen concentrations. This potential problem would be particularly associated with large gravel mine pits, which collect decaying organic matter and provide virtually no flow turbulence such that dissolved oxygen concentrations would be reduced within and downstream of the pit. Although reduced dissolved oxygen concentrations are probably not lethal to juvenile salmon, mortality may result from the combined effects of reduced dissolved oxygen concentrations with other stressors including high water temperatures, disease, contaminants, and predation. For example, many dead O. mykiss, Sacramento pikeminnow, Sacramento sucker, and riffle sculpins were observed in the Tuolumne River near the La Grange Bridge in early June 2002 (Walser, personal communication, see "Notes") when water temperatures were between 59 and 61 oF. Mortalities should not have occurred at these temperatures unless dissolved oxygen concentrations were unusually low in the dredged channel near the bridge.

Floodplain Inundation:

The highly regulated flows and the construction of dikes to convert floodplain to agricultural uses on the Stanislaus River have substantially reduced that amount of floodplain that is inundated annually. Although the extent or benefits of floodplain inundation have not been quantified in the Stanislaus River, floodplain inundation probably provides a rich source of terrestrial food for juvenile salmon and organic matter that helps generate more food in the river. Growth, survival, feeding success and prey availability for juvenile Chinook salmon were higher in the Yolo Bypass, the primary floodplain of the lower Sacramento River, than in the adjacent mainstem channel in 1998 and 1999 (Sommer and others 2001). Most of the remaining functional floodplain in the Stanislaus River consists of approximately half-mile long, narrow strips that are inundated at flows of 1,500 cfs near Knights Ferry (RM 54), Frymire Ranch (RM 53), and Honolulu Bar (RM 47).

Predation:

Although predation of juvenile salmon by striped bass, largemouth bass (Micropterus salmoides), and smallmouth bass (M. dolomieu) is thought to be a major source of mortality in the San Joaquin River tributaries, the evidence does not fully justify the theory. EA Engineering, Science, and Technology (EA) conducted riverwide electrofishing surveys in the Tuolumne River in spring 1989 and 1990 (EA 1992) and concluded that largemouth and smallmouth bass are the primary predators of juvenile salmon. However, very few bass contained juvenile salmon in their stomachs except during May 1990 when 93,653 hatchery reared salmon smolts were released at Old La Grange Bridge for survival studies. The following table summarizes the results of EA's studies.

Sampling Dates	La Grange Flows (cfs)	% Largemouth Bass with juvenile salmon in their stomachs	% Smallmouth Bass with juvenile salmon in their stomachs	Origin of Juvenile Salmon
4/19 to 5/17, 1989	40 - 121	3.6% (2/56)	8.6% (5/58)	Naturally Produced
1/29 to 3/27, 1990	142 - 174	2.1% (2/97)	3.1% (1/32)	Naturally Produced
4/25 to 4/28, 1990	187 - 207	2.6% (2/76)	6.3% (1/16)	Naturally Produced
5/2 to 5/4, 1990	299 -572	26% (40/152)	33.3% (6/18)	CWT Hatchery

Although EA estimated that almost 70% of the tagged hatchery fish died during their three-day migration from the La Grange Bridge to the confluence with the San Joaquin River, presumably from predation, their study cannot be extrapolated