The underlying case began in 2005 when a coalition of fishermen, conservation, and tribal groups challenged the federal government's biological opinion on the 2004 Operations Criteria and Plan (OCAP) for management of the SWP and CVP. The 2004 OCAP significantly increased water exports from the Sacramento-San Joaquin River Delta over historic levels and instituted other measures, such as relaxing cold water flow requirements and eliminating nearly half of the remaining salmon spawning habitat in the upper Sacramento River. These changes reversed protections credited with saving endangered winter-run Chinook salmon from extinction and have contributed to significant declines in protected salmon populations since 2004.
On April 16, 2008, Judge Wanger ruled that the biological opinion approving operation of the state and federal water projects violated the Endangered Species Act. The judge relied on the federal National Marine Fisheries Service's (NMFS) own finding that the current operations of the projects "...result in the loss of 42 percent of the juvenile winter-run Chinook population, and proposed project effects are expected to result in an additional 3 to 20 percent loss of the juvenile population.."
NMFS also found that the plan to export more water from the delta, would kill up to 66 percent of Central Valley steelhead and 57 percent of juvenile spring-run Chinook salmon. The fisheries service acknowledged the increased water diversions and pumping would likely lead to the extinction of the spring-run in the Sacramento River and steelhead in the Central Valley. The court ruled the federal government's finding that the projects would not jeopardize listed salmonid species simply didn't square with the facts. In July 2008, Judge Wanger reaffirmed his earlier ruling and explicitly held that current water operations are jeopardizing the existence of the three species.
Prior to construction of the state and federal water projects, Chinook (or king) salmon and steelhead were abundant in the Sacramento and San Joaquin river systems. Salmon were, and still are, of great cultural and spiritual importance to the Winnemem Wintu Tribe and remain a major economic contributor to California's fishing industry.
Many dams were constructed up and down the western slope of the Sierra Nevada on every major river flowing into the Sacramento and San Joaquin rivers, blocking the upstream migration of salmon and steelhead to and from their historic spawning grounds. Of the 6,000 miles of historic steelhead spawning grounds, today only 300 miles remain. Friant Dam on the San Joaquin River resulted in the extinction of the spring-run Chinook salmon in that river. Shasta and Keswick dams on the Sacramento River blocked the winter-run Chinook salmon from their historic spawning grounds, forcing them to spawn in a 40-mile stretch of less favorable habitat below those dams.
Every year the pumping of huge volumes of fresh water out of the Sacramento-San Joaquin River Delta sucks in and grinds up juvenile salmon and steelhead as they attempt to migrate downstream and though the delta on their way to the ocean. As a result, Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, and Central Valley steelhead populations have plummeted from historic abundance and all three species are protected under the federal Endangered Species Act.