Three environmentalist groups filed a lawsuit alleging that to increase water flowing to farms and cities, state and federal regulators in the drought have repeatedly relaxed water-quality standards on the Sacramento-San Joaquin Delta to the detriment of its wild fish species.
The lawsuit filed in U.S. District Court in San Francisco claims the U.S. Environmental Protection Agency failed to enforce the Clean Water Act.
The Natural Resources Defense Council, The Bay Institute and Defenders of Wildlife say they sued in response to nearly two dozen decisions made by California’s State Water Resources Control Board that reduced water quality standards to increase water shipments to farms and cities.
The groups say the decisions have had disastrous consequences for native fish that were already struggling in the fragile estuary. Two species in particular, Delta smelt and winter-run Chinook salmon, are hovering on the edge of extinction.
“This is just becoming habit now,” said Kate Poole, an attorney for the Natural Resources Defense Council. “The agencies aren’t even trying to come up with ways to meet these requirements.”
Poole said the State Water Resources Control Board has an obligation to order cuts to water deliveries, even to senior water rights holders, when their diversions harm water quality. The lawsuit claims the EPA had an obligation to step in because of the state’s decisions.

An EPA spokeswoman had no comment. A Water Resources Control Board spokesman said he had no comment, but Thomas Howard, the board’s executive director, said earlier this week that he didn’t think the allegations raised by the environmentalists had merit.
Environmentalists have long argued that excessive human demand for Delta water is the primary reason for the ongoing decline in fish populations. Pumps at the southern end of the Delta near Tracy deliver Sacramento Valley water to 19 million Southern Californians and millions of acres of farmland in the San Joaquin Valley. Water also is diverted by farms and cities upstream of the Delta as well as inside the estuary.
The lawsuit contends the most recent example of regulators relaxing water-quality standards occurred this week. The state board approved a request by the U.S. Bureau of Reclamation and federal fisheries officials that lowered minimum flow and oxygen requirements on the San Joaquin River before it flows into the Delta.
Environmentalists say the decision will harm migratory fish, including federally protected steelhead, as well as fall-run Chinook salmon.
Poole said nearly 10,000 adult Chinook recently had made their way through the Delta into the San Joaquin River basin to spawn, so ample flows are critical right now because their offspring are trying to make it down the river to the Pacific Ocean.
“We’re not giving the juveniles a way to get out safely,” Poole said. “We’re basically hammering the fall run that did successfully make it up there to spawn.”
Fall-run Chinook make up the bulk of the fish caught by California’s $1.4 billion-a-year salmon fishing industry.

Howard, the Water Resources Control Board executive director, said he signed off on the plan because the drought has so depleted New Melones Reservoir that there’s a need to maintain enough cold water flows for fish to last throughout the rest of the year and into 2017.
New Melones, on the rim of the eastern San Joaquin Valley, is the state’s fourth largest reservoir. It’s at 27 percent of capacity.
The matter is complicated because two local irrigation districts, Oakdale and South San Joaquin, have senior water rights that entitle them to up to 600,000 acre feet of water from New Melones, said Shane Hunt, a spokesman for the federal Bureau of Reclamation.
Hunt’s agency operates New Melones Dam, but is a junior-water rights holder.
“At least where I’m standing right now the problem is that the only entity that has responsibility to meet those public-trust flows is the bureau,” Howard said, “and they don’t have the water.”
As part of the agreement, the districts will allow 75,000 acre-feet of water to flow into the San Joaquin River system, but that’s not enough to maintain the minimum standards.