By Bettina Boxall State regulators want to leave more water for fish and wildlife in the heavily tapped tributaries of the San Joaquin River, setting the stage for another bruising California water fight. The proposal to keep more water flowing in the Merced, Tuolumne and Stanislaus rivers could spread the pain caused by environmentally related water cuts to irrigation districts and cities that have largely escaped them, thanks to their location and seniority in the hierarchy by which the state allocates water rights. Officials with a stake in those rivers’ water came out swinging Thursday within hours of the release of new proposed flow standards. “Our community has never faced a threat of this proportion,” proclaimed a statement from the more than century-old Modesto and Turlock irrigation districts, which called the draft standards an “uncompromising, misguided plan” that would steal the region’s livelihood. The proposal by the State Water Resources Control Board focuses on major Sierra Nevada-fed rivers that much of the time lose 60% or 70% of their natural flow to dams and diversions. This water helps quench San Francisco’s thirst and waters crops on the east side of the San Joaquin Valley. And its diversion devastates populations of salmon and other native fish. “The cost to species has been enormous … We can’t ignore the flow needs anymore,” water board Chairwoman Felicia Marcus said. The draft plan, which could be revised after public hearings and comments, sets February through June flow standards of 30% to 50% of the water that would naturally course down the river beds if there were no reservoirs or diversions. An initial requirement of 40% could vary within that range depending on what other measures water users take to improve fish conditions. “Flow alone is not the answer,” said Les Grober, deputy director of the board’s division of water rights. Other harmful factors, such as loss of habitat, predation by nonnative species and high river temperatures could be alleviated by restoration programs and different water management practices, board officials said. Acknowledging the potential losses to irrigation districts and cities that depend on the tributaries for much of their supplies, the board is encouraging users to come up with voluntary plans to boost salmon populations and keep the flow requirements in the lower range. The 40% standard is greater than an earlier board proposal but significantly less than the 60% recommended for fishery protection in a 2010 board report. That number did not take into account nonenvironmental needs, which board officials said it is their duty to consider. Marcus called the plan an attempt at “balancing competing interests — to share the river with each other and with nature.” The tributary proposal is just one part of a major update of water quality standards for the Sacramento-San Joaquin Delta and its sprawling watershed. The agency will also develop new flow requirements for the Sacramento River and for outflow from the delta to the sea — steps that will also be controversial. “We are long overdue for this tune-up and we need to act,” Marcus said. While the Oakdale and South San Joaquin irrigation districts condemned the flow proposal as “the worst kind of government overreach,” a fishing group called it “a historic step to right a wrong.” “Leaving a little bit more water in the San Joaquin River and its tributaries is absolutely benefiting humans since that water will translate into more salmon fishing and salmon for people to eat,” said John McManus, executive director of the Golden Gate Salmon Assn. Doug Obegi, a staff attorney with the environmental group Natural Resources Defense Council, said the 40% standard falls short of what is needed to build sustainable fish populations in the heavily drained rivers. Though diverters with senior water rights are likely to challenge the board’s authority to make them leave more water in the rivers, Obegi noted that the courts have upheld the board’s power to protect public resources. “It’s not a legal question,” he added. “It’s a political question.” Holders of senior water rights in the delta watershed have had to take steps to protect native fish, such as screening river intakes or altering diversion schedules. But they have been generally immune to the sometimes significant environmental cuts imposed on southbound delta deliveries to the western San Joaquin Valley and Southern California. “This is the first time San Francisco is potentially going to be on the hook” to boost river flow, Obegi said.