A state board proposes to help fish by reducing average annual diversions on the Tuolumne River by 15 percent and on the Merced River by 13 percent.
The idea drew protest Thursday from water suppliers, including the Modesto and Turlock irrigation districts, which argue that the reductions would be especially tough in dry years.
A fishing industry leader, on the other hand, said even more water is needed in the rivers.
The proposal came from the State Water Resources Control Board, which aims to improve conditions for salmon and other life in the lower rivers as well as the Sacramento-San Joaquin Delta.
Most of the increased flows would happen from February through June each year, when young salmon are heading out to the Pacific Ocean, but the districts are trying to store water for summer.
"Restoring our fisheries is not a problem that can be solved by simply throwing more water down the river," said Allen Short, executive director of the San Joaquin Tributaries Authority, in a news release.
Short, who retired as the MID's general manager last month, now heads a group made up of several water suppliers on the Tuolumne, Merced and Stanislaus rivers.
They include the Modesto, Turlock, Merced, Oakdale and South San Joaquin irrigation districts, as well as the San Francisco-owned system that supplies many Bay Area residents.
The proposal would reduce average annual flows in the Stanislaus by 3 percent because it already contributes a greater share to fisheries than the other rivers. This did not ease the concerns of the critics, who said the overall plan still relies too much on increasing flows.
Under the proposal, which the state board could approve in August, the February-June flows on all three rivers would increase to 35 percent of the natural conditions before they were diverted.
The rivers need to run at twice that volume if the depleted fisheries are to recover, said Zeke Grader, executive director of the Pacific Coast Federation of Fisherman's Associations.
Commercial fishermen in the San Francisco-based group endured shutdowns of salmon fishing in 2008 and 2009.
"I don't think anyone wants to do away with agriculture, but at the same time, we need to take a look at what kind of crops we are growing," Grader said.
The state board said the increased flows would cut farm income in the region by just 1 percent. Reduced water supplies would likely mean that farmers turn from lower-value crops such as corn to higher-value crops such as almonds, the board said.
The irrigation district group said fish would benefit more from nonflow measures such as restoring streambeds, reducing predation by non-native striped bass, changing ocean fishing rules and improving hatchery practices.
"If you're going to ask people to make this serious sacrifice," Short said, "you'd better be darn sure you know what the benefits are, and the fact is, they have not even estimated what, if anything, will be achieved by increasing flows."
The proposal would shift much of the districts' hydroelectric generation to earlier in the year, when it is of less value, but the loss would not be substantial, the board said.
The proposal comes as the MID and the TID are seeking a new federal license for the Don Pedro hydropower plant. This process could result in increased flows downstream, but managers have said they should not be on top of what the state board requires.
Bee staff writer John Holland can be reached at firstname.lastname@example.org or (209) 578-2385.
March 5: Deadline for written comments on proposed flows in lower Stanislaus, Tuolumne and Merced rivers
March 20: Workshop on proposed flows at State Water Resources Control Board, Sacramento; time to be announced
May 3: Draft final proposal to be released for comment
Aug. 6: Possible final vote
ON THE NET: www.waterboards.ca.gov/ waterrights/water_issues/programs/bay_delta