The contentious struggle to restore threatened fisheries in the San Francisco Bay-Delta and the Central Valley has focused mostly on reducing the amount of water exported from the Sacramento-San Joaquin Delta to farms and Southern California cities. That’s now changed.

The State Water Resources Control Board has asked San Francisco and other communities that withdraw water from rivers that feed into the delta from the south to be part of the solution.

Declaring that “the Bay-Delta is in ecological crisis,” the state water board has proposed leaving 40 percent of the natural flow of these rivers untouched. Water agencies will either have to develop new supplies or make do with less, especially in dry years when water supplies are at a premium.

San Francisco derives 85 percent of its supply from the largest of these rivers, the Tuolumne. The city and county of San Francisco operates three reservoirs in the upper watershed, including the controversial Hetch Hetchy Reservoir in Yosemite National Park. San Francisco itself uses only one-third of this supply, and sells the rest to other Bay Area communities.

Downstream, the Turlock and Modesto irrigation districts use about three times as much Tuolumne water as San Francisco. The irrigation districts own and operate Don Pedro, by far the largest reservoir on the Tuolumne. San Francisco paid the irrigation districts one-half of the cost of Don Pedro’s construction in exchange for “water bank” storage credits. The Don Pedro agreement also specifies that any future increase in required flows on the Tuolumne might be apportioned 51.7 percent to San Francisco and 48.3 percent to the irrigation districts.

Water agencies rarely give up any of their supply voluntarily.

The irrigation districts have already stirred up fierce local opposition to the state water board’s proposal. San Francisco is opposing the proposal as well — even though Bay Area support for protecting salmon and other fisheries dependent on healthy flows into the delta is strong. The final outcome is anything but certain, but major changes are indeed expected.

The state water board does not specify how the burden of compliance should be shared. Board Chairwoman Felicia Marcus, with explicit support from Gov. Jerry Brown, has asked the various agencies to work together on a cooperative solution, but warned that the board has the power to impose a solution should the agencies fail to do so.

The board has suggested specific alternative sources of supply for San Francisco, along with discussion of their feasibility and analysis of their cost. None is easily accomplished, but all are possible.

In recent decades, California cities and farms have made significant changes in how they store, move and use water, often because of collapsed fisheries. Central Valley farmers have installed enough drip irrigation to reach the moon and back. Innovative cities have built surface reservoirs closer to urban populations, recharged local groundwater basins and paid distant farmers to recharge the groundwater beneath their lands. Cities are also increasing their use of recycled wastewater — a supply that is virtually drought-proof. The list goes on.

San Francisco has pursued very few of these options. It has not needed to. To date, the city has not been required to help solve problems in the San Francisco Bay-Delta. It has also avoided requests to consider alternatives necessary to restore Yosemite’s Hetch Hetchy Valley.

The Bay-Delta Plan lays out water quality protections for California drinking, irrigation and fisheries. The proposed update analyzes the impacts, benefits and costs of the proposed revisions. The state water board must consider all beneficial uses of water and balance those interests.

The legal mandates within the Bay-Delta Plan require, however, that all parties who divert water within the watershed be part of the solution. Others have done their part, now it’s San Francisco’s turn.

Spreck Rosekrans is executive director of Restore Hetch Hetchy. To comment, submit your letter to the editors at http://bit.ly/SFChronicleletters.