For nearly three decades, Westlands Water District received almost 100 percent of its water allocation from the federal Central Valley Project. Water allocations began to decrease in 1992, thanks to environmental legislation, but there was still enough to grow crops and make a living. However, in February the U.S. Bureau of Reclamation, which oversees the Central Valley Project, announced farmers south of the Sacramento-San Joaquin Delta would receive no water. In the end, residents received a drastically reduced amount.

Westlands, which receives all of its water from the CVP, serves about 50,000 people in western Fresno and Kings counties, most of whom depend on agriculture. In March, Westlands and the San Luis & Delta-Mendota Water Authority, an organization that represents CVP water users and of which Westlands is a member, sued the U.S. Department of the Interior, the U.S. Fish and Wildlife Service and the U.S. Bureau of Reclamation.

The water agencies sued the federal government over a document the Fish and Wildlife Service released in December 2008. The biological opinion examined the effects of operating the CVP and the State Water Project, the state’s two main water systems, on Delta smelt, a threatened fish under the federal Endangered Species Act. The act requires Fish and Wildlife to produce a biological opinion if a federal project could jeopardize an endangered species’ existence.

In the biological opinion, Fish and Wildlife concluded the two projects are “likely to jeopardize the continued existence of the Delta smelt and adversely modify its critical habitat.” The agency recommended the “reasonable alternative” of restricting pumping to protect the tiny native fish. Once abundant, the Delta smelt’s numbers have dropped since 1999 to their lowest level on record in 2008, according to Fish and Game.

The two water districts sued, claiming Fish and Wildlife is not following the law or applying the best science under the Endangered Species Act. Consequently, the agency is inflicting suffering on the water districts’ customers without helping the fish, says Daniel O’Hanlon, lead attorney on the case with Kronick Moskovitz Tiedemann & Girard in Sacramento. The lawsuit argues there is a “pervasive bias” in the 2008 biological opinion — that Fish and Wildlife favors restricted pumping even though that action hasn’t caused the species’ numbers to rise. The U.S. Department of Justice declined to comment, citing the pending legislation.

While the CVP eventually gave 10 percent of water to farmers south of the Delta this year, the amount was the lowest on record for that group and forced the fallowing of thousands of acres.

The plaintiffs are asking Judge Oliver Wanger to find the biological opinion invalid and force Fish and Wildlife to rewrite it, easing pumping restrictions and restoring some water to farmers. More than two thirds of Californians rely on the Delta, the heart of the state’s water supply, for some portion of their drinking water. Most of the state’s water is collected in Northern California before being pumped through the Delta to users in the Central Valley, San Francisco Bay area and Southern California. Delta exports have been curtailed for many customers this year. “The restrictiveness of these measures is way out of proportion to anything that the science would say is of material benefit to the overall population,” O’Hanlon says.

The plaintiffs agree that pumping damages Delta smelt, but according to O’Hanlon, it is a “relatively small portion.” Most of the smelt aren’t near the pumps and aren’t affected by them, he says. There are other causes for the smelts’ decline, including pollution and invasive species, the lawsuit argues. Restricting pumping has not caused the fish species numbers to rise, it says.

Sarah Woolf, spokesperson for the Westlands Water District, says her agency sued the federal government because the biological opinion didn’t consider the environmental and human impacts of not being able to farm because of a lack of water. Westlands estimates, with ongoing pumping restrictions to protect the Delta smelt, it will average 35 percent of its 1.2 million acre-feet annual allocation, an amount she says is unsustainable. The district’s roughly 700 farms fallowed 260,000 of their 600,000 acres because of this year’s water shortage, a record low.

Woolf says she doesn’t expect the pumping restrictions to be lifted entirely but hopes for some relief. “There has to be a balance between the fish that are being impacted and the … loss of employment, loss of business, loss of ability to service the needs of a population,” she says.

In court documents, the U.S. Department of Justice argues unlimited pumping will increase the number of Delta smelt caught at the pumps and “could cause irreparable harm to the species.”

The government says the farmers have failed to show that pumping restrictions — not drought and recession — are harming farmers and others on the San Joaquin Valley’s west side. Delta water exports have been reduced this year not only to protect the Delta smelt, but also because California is in its third year of a drought, the lawsuit says.

A final ruling is not expected until after March.