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The Stanislaus River Restoration Plan Information Site
CHAPTER 1 INTRODUCTION

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:

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:

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.

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Introduction
Public Outreach
 Existing River Conditions
Conceptual Models Of Potentially Limiting Factors
 Prioritized Restoration Actions and Research
Literature Cited
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