Federal regulators on Tuesday denied a petition by environmentalists to put a large minnow back on the list of endangered species, essentially backing an unprecedented Bush-era decision to remove Sacramento splittail from the list. Environmentalists called the decision "inexplicable" and said they would seek to overturn it in court.

Sacramento splittail, which were the most abundant fish in lower Walnut Creek during a survey by state biologists in the late 1990s, can be found from San Pablo Bay, up through the Delta and in Central Valley rivers.

Although environmentalists say its population has been in decline, the U.S. Fish and Wildlife Service concluded that it could not discern a trend because fish counts are unreliable and their numbers go up and down dramatically in response to the amount of rain and snow in any given year.

"Because of the fluctuations in their numbers, it's difficult to discern a long-term trend," said Dan Castleberry, field supervisor for the service's San Francisco Bay-Delta field office.

Regulators concluded that enough of the fish can survive droughts to permit splittail to rebound in wet years.

"I don't see this conclusion being scientifically justified," said Tina Swanson, executive director of the Bay Institute and an expert on Delta fish. Swanson called the decision "inexplicable."

"Every single survey shows either record or near record lows," she added.

The Center for Biological Diversity, a Tucson, Ariz.-based environmental group that last year sued federal regulators to reconsider their 2003 decision to remove the fish from the endangered species list, said it would challenge Tuesday's decision.

Federal regulators relied on results of computer modeling rather than surveys in which biologists catch and count the fish because the fish surveys were not specifically designed to count splittail.

Biologists have disagreed for years about whether the fish belongs on the list of endangered species.

Including it on the list would add a layer of complication to an already dizzying set of issues in the Delta, where a biological collapse is putting pressure on water supplies statewide.

Splittail were designated a threatened species in 1999, but farm districts sued and regulators were ordered to reconsider the decision.

In 2003, the Fish and Wildlife Service's top official in Sacramento overruled his biologists and decided to remove the fish from the list. That decision was sent to Washington, D.C., where Julie MacDonald, a former deputy assistant Interior secretary, heavily edited the report even though it could affect her economic interests in the family farm near Dixon.

MacDonald resigned in 2007 in the wake of a blistering report by the department's inspector general's office, which found she was inappropriately interfering with agency biologists and providing information to interest groups.

The Times first reported her involvement in the splittail decision. A follow-up report by the Interior Department's inspector general's office confirmed the Times' reporting and said her involvement amounted to a conflict of interest.

Mike Taugher covers the environment. Contact him at 925-943-8257.