While the delta smelt serves no commercial purpose, decisions impacting its habitat extend directly to the interests competing for California’s water: farmers, fishermen and environmentalists.

“This is the most contested water problem in California,” said Jeffrey Mount, a water policy expert with the Public Policy Institute of California. “The fundamental water question is how much water you allocate to the environment and how much you allocate to farms. This tilts the balance to farms. And this was at the directive of the Trump administration.”

Environmental groups again accused the administration of favoring preferred constituents over science.

The conclusion “flies in the face of the best available science, which indicates that stronger protections are needed to prevent the extinction of our native fish and wildlife, like endangered winter-run chinook salmon and delta smelt, particularly in light of the effects of climate change,” said Doug Obegi, an expert in California water law with the Natural Resources Defense Council, an advocacy group.

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It also brings both Mr. Bernhardt and his former lobbying client a big step closer to the outcome they have sought for years.

From 2011 to 2016, Mr. Bernhardt lobbied on behalf of California’s Westlands Water District, a state-chartered organization representing about 1,000 large farmers in an area of central California the size of Rhode Island. During those years, Westlands, which was his largest client, paid Mr. Bernhardt’s firm $1.3 million.

The group’s chief lobbying goal was to lift federal environmental protections to allow California’s fickle water supply to be used consistently to irrigate Central Valley almond, pistachio and cotton farms. As Westlands’ lawyer and lobbyist, Mr. Bernhardt pressed Congress for legislation to weaken Endangered Species Act protections on the delta smelt. He also joined a legal petition asking the Supreme Court to take up a case seeking to weaken those protections.