So little water is flowing from the rivers that feed the estuary, which includes the Sacramento-San Joaquin River Delta, Suisun Marsh and the bay, that its ecosystem is collapsing, scientists who conducted the study say.

Human extraction of water from the rivers is not only pushing the delta smelt toward extinction, they say, but also threatening dozens more fish species and many birds and marine mammals, including orca whales, that depend on the estuary’s complex food web.

The findings by scientists at the Bay Institute, an environmental group, underline conclusions already reached by state regulators and are intended to buttress the environmental case for potentially drastic water restrictions in San Francisco and other parts of the Bay Area, and among farmers in the northern San Joaquin Valley.

The State Water Resources Control Board moved last month to require that Californians leave far more water — 40 percent of what would naturally flow during spring — in the San Joaquin River and its three main tributaries, the Tuolumne, Merced and Stanislaus rivers, in an effort to save fish species.

That would double the amount of water protected from human use in most years, according to the board. Last year, only 10 percent of the San Joaquin River, the second-largest in the state, reached the delta, as the rest was diverted or stored upstream. The Tuolumne, which is San Francisco’s main water supply, is one of the state’s most over-tapped rivers, with about 80 percent of its normal flow directed to human uses.\

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