State wildlife officials said the estimates are for fish that spawned naturally in rivers and don’t include losses of hatchery-raised fish.

(There is a caveat to the estimated losses of winter-run Chinook. State officials say they base their calculations on fish that are the size of winter-run Chinook rather than those that are genetically confirmed to be this type of salmon. As a result, officials say, some of the estimated losses are actually different types of salmon.)

The Department of Water Resources “is closely monitoring the collection system at the fish screens in front of the State Water Project pumps in the south delta,” said Karla Nemeth, the agency’s director.

“The majority of Chinook salmon and steelhead collected at the fish screens are collected alive and transported downstream of the pumps. We have been adjusting pumping operations to protect listed and endangered species,” Nemeth said in an email. “However, [State Water Project] operations have never been this restricted in a wet year as they are this year. These restrictions are keeping us from being able to capture and store the water that we need if we see a return to drought conditions.”

The pumps that supply the State Water Project have been operating far below their capacity over the past three months. Agencies that receive supplies have been told to plan for 30% of their full allocations this year.

The permits and biological opinions that govern state and federal pumping operations include measures aimed at limiting the deaths of fish. In response to the losses, state and federal officials have been discussing measures being taken to protect fish.

Rosenfield said the water agencies aren’t doing nearly enough and argued that the losses put them in violation of permits.

“If you and I were out there killing hundreds and thousands of endangered fish, we’d be in jail,” Rosenfield said. “They’re not doing everything they can do to prevent the harm and mitigate the damage. There’s an opportunity to protect these fish by reducing water exports. It’s urgent ... and they’re doing nothing.”

The environmental and fishing groups — which include Defenders of Wildlife, the Bay Institute, Golden State Salmon Assn. and the California Sportfishing Protection Alliance — pointed to notes from a March 6 meeting at which officials from the National Marine Fisheries Service proposed reducing pumping to very low levels “as soon as possible, for a minimum of five days, and then reassessing.”

The groups said that despite this advice from fishery officials, the Department of Water Resources and federal Bureau of Reclamation “ignored these recommendations and continued to export water at rates that killed thousands of imperiled fishes.”

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