The federal government is suing the State of California over a water grab plan to increase water flows in the Lower San Joaquin River that has a high likelihood of New Melones Reservoir — based on the planned diversion and historic hydrology on the Stanislaus River Basin — going dry 12 times every 95 years.

If implemented the plan would cut back available water to 52,000 acres of farmland within the South San Joaquin Irrigation District as well as the cities of Manteca, Lathrop, and Tracy. In drought years the potential would exist for severe rationing. The same consequences face Oakdale Irrigation District. The two districts share legally adjudicated water rights to the Stanislaus River watershed that supersedes any other jurisdictions including the state and federal governments.

 The state water plan is designed to increase Chinook salmon populations. The SSJID and OID have tried to share more than a decade of scientific research that demonstrates there are more effective ways at boosting the survival rates of native salmon.

The U.S. Department of Justice filed suit Thursday in Sacramento federal court to block the contentious plan approved in December to increase river flows in the San Joaquin River and three tributaries — the Stanislaus, Merced, and Tuolumne rivers — to help revive dwindling salmon populations. The lawsuit said the plan was arbitrary and the state failed to analyze impacts on the environment and would reduce water coming out of the New Melones reservoir for farms, cities, businesses and hydroelectric operations.

“SSJID appreciates the Department of the Interior’s decision to challenge the State Water Resources Control Board’s Water Quality Control Plan,” SSJID General Manager Peter Rietkerk said. “Environmental and human water supply needs from the Stanislaus River hinge on a sustainable operation of new Melones. Unfortunately, the state’s current plan does not offer a sustainable operation, nor balance the river’s complex water supply needs.  SSJID echoes Interior’s concern about the impacts of the state’s plan, and hopes a more balanced solution will emerge through the state’s voluntary settlement process.”    

The SSJID and OID were in the midst of negotiating with the state to find a more effective solution that had less of an impact on cities and farming when the state board in December voted 4-1 to go with the plan

The environmental analysis “hid the true impacts of their plan and could put substantial operational constraints on the Department of the Interior’s ability to effectively operate the New Melones Dam, which plays a critical role in flood control, irrigation, and power generation in the Sacramento region,” said Assistant Attorney General Jeffrey Bossert Clark said in a statement.

The federal government’s lawsuit follows a suit filed last month in state court by the California Farm Bureau Federation to block the plan.

The plan that is targeted in the lawsuit is part of a larger effort to protect the Sacramento-San Joaquin Delta, which state officials called an “ecosystem in crisis.”  

Once-thriving fish in the Delta, which flows out to San Francisco Bay, have plunged from some 70,000 adult Chinook salmon returning to the San Joaquin basin in the fall of 1984 to just 10,000 in 2017. 

The SSJID and OID do not dispute that. They have pointed out the increased water flows as the state envisions would increase the salmon numbers now pegged at 10,000 by just over 10 percent based on the state’s own analysis and will bringing widespread economic losses to the region.

The plan as passed would increase unimpaired flows to 40 percent in a bid to expand the Chinook salmon population. Some environmental groups supported the plan, while other conservation groups and fishing groups said it fell short in providing enough water for habitat.

The decision that the board argued could be adjusted if water users along the Stanislaus and Merced rivers would agree to concessions to improve fish habitat as agencies along the Tuolumne River did has been characterized by state officials as one that would make farmers in the western San Joaquin Valley lose some of the water stored behind reservoirs such as New Melones they have contracted for but has rarely acknowledged the loss to farmers and cities in the northeastern San Joaquin Valley in San Joaquin, Stanislaus, and Merced counties. Property owners and residents in the three counties have legally adjudicated pre-1914 water rights in addition to having developed reservoirs to use those water rights long before out-of-basin users such as west side farmers, San Francisco and other Bay Area cities entered the picture.

The Stanislaus River is unique in the San Joaquin River basin. The river is already flowing at 30 to 35 percent unimpaired flows — significantly more than most rivers in the state. 

Rietkerk noted that “while we see some marginal benefit to additional flows, we’ve also experienced water supply impacts and fishery declines because current river operations cannot sustainably be manage for both.”

The SSJID and OID have more than a decade of scientific fish studies on the Stanislaus River and have invested in habitat improvement for salmon. That has not been done on either the Merced or the Tuolumne nor has the state done extensive research related to fish specifically on the three rivers.

Rietkerk said the two districts have data that supports a more moderate increase in impaired flows as well as their timing that would be much more beneficial than the state’s plan.

 At the same time another mandate from Sacramento — groundwater sustainability meaning more water cannot be pumped from an aquifer in a given year than what is replenished — will sustainably impact water supplies in San Joaquin County. 

George Kostyrko, a spokesman for the water board, said the agency looks forward to defending the plan that involved years of analysis and public input.

The Associated Press contributed to this report.