SACRAMENTO, Calif. — A Sacramento judge upheld a decision by California’s water regulator to cut back agricultural and municipal water use from the San Joaquin River. The decision could lend support for future regulations in the rest of the Sacramento-San Joaquin River Delta system.

It comes amid declining fish populations and increasing pressure on water supply due to climate change. But rather than move forward with strict regulations, the state agency is considering a plan pushed by Gov. Gavin Newsom that would grant water districts more flexibility.

The Friday ruling by Sacramento County Superior Court Judge Stephen Acquisto rejected a litany of lawsuits by water districts against the State Water Resources Control Board’s plan to boost river flows and help revive struggling native fish populations.

Agencies that filed suit against the state’s plan include large agricultural water suppliers such as the Modesto Irrigation District, Westlands Water District and Merced Irrigation District, as well as the San Francisco Public Utilities Commission and city of Modesto.

The judge ultimately supported the agency’s water quality plan for the lower San Joaquin River — including the Tuolumne, Merced and Stanislaus river tributaries — which set specific goals to protect water flows for key fish species such as chinook salmon and steelhead trout.

In his ruling, he wrote there is “more than enough valid scientific evidence in the record to support the Board’s general conclusion that increased flows in the lower San Joaquin River and its three eastside tributaries are of critical importance to reviving and sustaining native migratory fish populations.”

He denied all the petitioner’s claims about the water board’s 2018 plan for the river that was passed with much controversy. That included complaints about the water board’s process and contentions that the agency had abused its regulatory authority.

In the San Joaquin River, which begins high in the Sierra Nevada and flows through the the northern San Joaquin Valley before reaching the ocean through the San Francisco Bay, sometimes more than 80% of its flow is diverted for farms and cities.

The Delta is ecologically ailing. Populations of salmon, delta smelt and other native species have been on a steep decline in recent years. Regulators shut down the fishing season last year because populations of fall-run Chinook salmon last year were so low.

Under its San Joaquin river plan, the water board would limit diversions during certain times of the year to between 50-70% of the river’s total flow. Lawsuits quicky followed after the decision. More than five years later, the rules have not been implemented.

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