RIO VISTA, Calif. — On a boat in the heart of California’s biggest river delta, a researcher pored over a sample of murky, weed-infested water, looking for a rare fish about the size of a finger. Spotting one, he shouted in triumph — then measured it and quickly tossed it overboard.

“They’re very fragile,” explained the researcher, Greg Nelson, who works as a biological science technician for the federal Fish and Wildlife Service, as the silvery fish darted away.

The tiny fish, known as the delta smelt, has helped touch off some of the most cataclysmic battles in California’s unending water wars. The delta that it inhabits lies in Northern California, at the confluence of mighty snow- and rain-fed rivers that drain into San Francisco Bay before their water heads out to the ocean. The rivers supply water through the delta for about two-thirds of Californians as well as vast tracts of rich farmland. But drought and the pumping of water to users as far away as Los Angeles have depleted the smelts and the delicate ecosystem they inhabit, prompting limits on the amount of water sent to farmers and cities — and sparking political warfare among farmers, cities, environmentalists and fishermen.

“We tend to say that this is the single biggest water management challenge that California faces,” said Ellen Hanak, a senior fellow at the nonpartisan Public Policy Institute of California. The debate over the delta, she said, ranks with those over other great national ecological landmarks, like the Everglades, the Great Lakes and Chesapeake Bay.