Local farmers are contending with severe cuts in their water supply after federal water pumps killed an unusually large number of endangered fish within the past few months.

Cities and irrigation districts have lost out on 775,000 acre-feet of their promised water supply since cuts began Dec. 7, according to the California Farm Water Coalition, a group that represents farm water users throughout the state, including irrigation districts on the West Side.

That’s about 250 billion gallons, enough to have grown nearly $1 billion in fresh fruits and vegetables or served the household needs of 4.5 million people for a full year, according to the coalition’s website.

“It’s having a terrible effect,” said Bill Harrison, general manager of the Patterson-based Del Puerto Water District, which serves about 45,000 acres of farmland between Vernalis and Santa Nella. “It’s making our forecast look very poor for the upcoming year. Every day that pumping is curtailed is lost supply for us.”

A federal pumping plant north of Tracy sent 250,000 fewer acre-feet of water into the Delta-Mendota Canal than usual, according to Frances Mizuno, assistant executive director of the San Luis and Delta-Mendota Water Authority, which operates the system.

The Delta-Mendota is part of the federal Central Valley Project conveyance system and provides water for several West Side irrigation districts.

“That 250,000-acre-foot reduction translates into a 15 percent drop in allocations of our project’s water to agricultural users,” Mizuno said last week

The remaining 450,000 acre-feet that had been diverted as of that time would have gone toward the State Water Project, which provides water for cities and irrigation districts via the California Aqueduct, she said.

Fish in trouble

The U.S. Fish and Wildlife Service restricted water pumping Feb. 8 based on the discovery that 228 adult smelt — protected under the federal Endangered Species Act — had been pulled into in pumps as of Feb. 6.

That number is about 75 percent of the 305 smelt the service is allowing to be killed by the pumps in 2013, based upon surveys of the fish population.

But those restrictions were loosened slightly Feb. 12 and even further Feb. 15, when it became clear that no additional smelt had been sucked into the pumps since Feb. 6, causing Fish and Wildlife officials to wonder whether conditions were improving for the finger-long fish.

On Tuesday, Feb. 19, three out of five pumps were operating at the federal pumping plant, said Pete Lucero of the federal Bureau of Reclamation, which oversees the Central Valley Project. The station had been down to just one pump Feb. 8.

Problems for the fish emerged in late December, when a series of storms made the Delta waters cloudy with sediment.

Schools of smelt, attracted to murky conditions, followed a plume of turbid water from the Sacramento River south into the San Joaquin River and got sucked into pumps in the process, said Steven Martarano, a spokesman for the U.S. Fish and Wildlife Service.

A Smelt Working Group comprising biology experts from various state and federal agencies has met weekly since December to decide on measures such as pumping curtailments to prevent too many smelt from being killed.

The group’s purpose is to ensure that smelt numbers are preserved in accordance with guidelines in a biological opinion the U.S. Fish and Wildlife Service issued in 2008.

Scientists say the Delta smelt are an “indicator species,” meaning that if they are in trouble, the health of the entire Delta is in trouble.

Mizuno said pumping restrictions to protect the smelt will continue into March, when protection for the Delta’s threatened winter-run salmon will begin.

She anticipated that pumping restrictions would continue until early July and that the water authority would operate one to three pumping units instead of five units at full capacity.

Irrigation districts alarmed

If water allocations do not improve for farmers, Harrison, the local water district manager, predicts this year could be like 2009, when water issues became politically charged.

“It could get very ugly,” Harrison said.

Even in wet years, it’s typical that recipients of pumped water do not receive their fully contracted supply. And when it’s a dry year, those receiving water pumped from the Delta are the first to have their supply restricted.

In April 2009, farm workers and farmers marched from the city of Mendota to the San Luis Reservoir in protest after fields were left dry and farm workers jobless because federal Central Valley Project water allocations south of the Delta were capped at 15 percent of normal.

In 2012, by contrast, irrigation districts south of the Delta that rely on federal water received 45 percent of the water specified in their contracts.

At the start of this water year, with reservoir levels still relatively high, officials hoped for allocations up to 35 or 40 percent.

But with curtailed pumping and only light rainfall since Jan. 1, many farm water experts are expecting 20 percent to 30 percent allocations this year.

Allocations will likely be announced early next week, Lucero said.

Harrison said farmers can respond to limited water supplies by growing fewer row crops than in the past, but they must irrigate their orchards, which are starting to bloom. Without water, trees will ultimately die.

“The trees are starting to wake up, and they need water when they do,” Harrison said.

State officials put hopes in canal

The problems with the smelt have given ammunition to those who support delving twin tunnels to channel water from the Sacramento River directly south to pumping plants, instead of allowing it to flow through the Delta.

Gov. Jerry Brown’s office has estimated the cost of the project at $14 billion.

Modeling by the state Department of Water Resources shows that if the tunnels had been in place this winter, the state and federal water projects could have sent south about 700,000 acre-feet of additional water between Nov. 1 and Jan. 31, while still meeting all water quality and Endangered Species Act requirements, according to a release issued by the state’s Natural Resources Agency.

“This winter provides a case study in why we must find a better way to balance needs in the Delta,” said state Department of Water Resources Director Mark Cowin. “The current plumbing configuration in the Delta serves neither people nor fish and wildlife well.”

Opponents of the canal, especially farmers with longstanding water rights north of Tracy and west of Stockton who rely on water directly from the Delta, say the plan would degrade water quality throughout the Delta.

Federal and state water and wildlife officials are talking about ways to ease the impact of reduced pumping levels on water users but have no concrete answers yet.

Harrison, of Del Puerto Water District, said he anxiously awaits the Bureau of Reclamation’s allocation figures for Central Valley Project contractors in the meantime.

“We’re nervous, but we’re hoping for improvements here in the near future,” Harrison said.

• Sam Matthews, Tracy Press publisher emeritus, contributed to this report.

• Contact Jonathan Partridge at 892-6187, ext. 26, or jonathan@pattersonirrigator.com.