California farms have dried up a river for months. Nobody stopped them.

During California's most recent drought, officials went to great lengths to safeguard water supplies, issuing emergency regulations to curb use by thousands of farms, utilities and irrigation districts.

It still wasn't enough to prevent growers in the state's agricultural heartland from leaving several miles of a major river dry for nearly four months in 2022, in a previously unreported episode that raises questions about California's ability to monitor and manage its water amid worsening droughts. .

It is not uncommon for California farmers and other water users to see streams suck down to a trickle in some places during dry spells. But the severity and duration of the Merced's 2022 decline, where one flow gauge showed no water flowing past it nearly every day from June to early October, stood out even to experts.

“I was very surprised to see a river of this size with no water,” said Jon Ambrose, a biologist with the National Oceanic and Atmospheric Administration's Fisheries Service, who visited the dried-out Merced riverbed in August. “This is just not something we see. This is not something that should be considered normal.”

The Merced River originates in Yosemite National Park. It flows through glacier-carved canyons and winds through the Central Valley for about 60 miles before emptying into the San Joaquin River, which feeds the southern half of the valley.

California's top water regulator, the State Water Resources Control Board, learned of the bone-dry conditions in the lower Merced in late October 2022, only after they had begun to ease, said Erik Ekdahl, deputy director of the board responsible for water rights, in an interview this week.

In investigating the case, the board has so far determined that the river most likely dried up because people used legal water, Mr. Ekdahl said. In other words, it appears that local farmers did not violate the administration's drought controls that year by slurping up every last drop.

“That's where the layman would immediately say, 'How can this happen?'” Mr. Ekdahl said. The reason, he said, is that in times of drought, California's water system is more focused on protecting the rights of water users than helping the environment. In general, “you can use the water you are authorized to use under your license or permit until you are specifically told not to.”

California became an agricultural power by taming its rivers and dividing their flows. But as a warming climate intensifies the state's flood and drought cycles, the water distribution system is under strain.

The state accords a high degree of privilege to senior users, or to those who have been exploiting and using the rivers' flows for a long time. This has helped encourage large investments in irrigation. Now, however, virtually every drop is being claimed for one purpose or another, and officials are finding it increasingly difficult to manage supplies and protect the environment without harming the interests of established growers and other users.

California was in its third straight year of drought in the summer of 2022, when officials from NOAA Fisheries and the state Department of Fish and Wildlife found miles of the lower Merced severely dry. The upstream part of the river was still flowing strongly, current meters showed. But by the time it neared its confluence with the San Joaquin, it had become a series of intermittent pools, endangering endangered fish species including steelhead and Chinook salmon.

“Our species is on the brink of extinction,” said Monica Gutierrez, a biologist with NOAA Fisheries who visited the Merced in August. “We cannot afford to have a dry riverbed for another year.”

According to state data, water users in lower Merced include dairies, almond farmers and vineyards that are part of E. & J. Gallo Winery, which calls itself the world's largest family-owned wine and spirits company. A spokeswoman for Gallo declined to comment.

California's 2022 drought response reduced supplies to many water users in the San Joaquin watershed, but not all. Many of the oldest users, or those who claim to have been using water the longest, were not cut off.

Even if the state water board had been aware of the Merced's withering conditions earlier that summer, it could have taken months to issue new regulations to protect the river, said Mr. Ekdahl, the board official. Imposing new rules to prevent the country from drying out in the future would also be a long and complicated process, he said.

“A dry river is a catastrophe,” said Keiko Mertz, policy director of Friends of the River, a conservation group in Sacramento. “The water board must anticipate, manage and prevent this from happening.”

California's water board doesn't have the staff needed to monitor river levels statewide, said Nell Green Nylen, a water policy researcher at the University of California, Berkeley. As a result, she said, “I suspect there are smaller streams all over the state, and maybe even some larger ones, where this kind of thing happens all the time.”