The Stanislaus River originates in the western slopes of the Sierra Nevada and is one of the largest tributaries of the San Joaquin River. The Stanislaus River is 113 miles long and covers an area of 1,075 square miles. The habitat currently available to salmonids on the Stanislaus River has been severely limited and impacted as a result of human activities over the past hundred years. Because of the significant impacts to habitat on the Stanislaus River, spring-run Chinook and viable populations of steelhead have been nearly extirpated from the watershed. Steelhead are present but only in low numbers. Installation of the Goodwin, Tulloch, and New Melones Dams has been the primary cause of depleted, degraded habitat (See this amazing story map on Central Valley dams). The Stanislaus River has been extensively dammed and diverted. The lower Stanislaus River has been extensively developed to provide water, hydroelectric power, gravel, and conversion of floodplain habitat for agricultural and residential uses. While the upper reaches of the lower Stanislaus River (below Goodwin Canyon) remain relatively undeveloped, the river floodplain below Knights Ferry (with the exception of a narrow riparian border) has been converted to urban and rural development or used for agriculture. By 1994, it was estimated that approximately 50 percent of the riparian corridor along the lower Stanislaus River had been converted for agricultural, mining, and urban uses. The Stanislaus River historically had 113 miles of anadromous fish habitat, but currently only the lower 58 river-miles are accessible to anadromous fish, with access terminating at Goodwin Dam. Although records on anadromous salmonids in the San Joaquin tributaries are sparse, the Stanislaus River still provides valuable spawning and rearing habitat for fall-run Chinook salmon and steelhead. Compared to historic conditions, the area of suitable salmonid spawning and rearing habitats has been substantially reduced due to anthropogenic influences including dam construction, in-river aggregate mining, and the conversion of floodplain habitat for agricultural uses. Gold and aggregate mining also have had a detrimental effect on spawning and rearing habitats in the Stanislaus River. Isolation of floodplain and riparian habitats from the Stanislaus River by dikes also has had a negative impact on salmonid spawning and rearing habitats.
The Stanislaus River is included on the federal Clean Water Act list of impaired water bodies due to pesticides, water temperature, toxicity and mercury contamination. Fall run Chinook salmon are federally listed as a species of concern. Steelhead are federally listed as threatened. Preventing the extinction of salmon and steelhead requires restoration of priority habitat conditions (listed in the Snapshot Restoration webpage) and consistent, funded monitoring of these fish populations.