Despite the teeth gnashing and political posturing that suggests protecting fish is drying up water supplies, Delta water sent to farms and cities hit an all-time high this year.

Another record was set too: 9 million Sacramento splittail fish were collected at the giant Delta pumps near Tracy.

The records show that characterizing the long-running fight over Delta water as one in which regulations are wiping out those who rely on it is not necessarily true.

New measures to protect fish indeed have affected water supplies, but most of the cuts to date have been due to drought.

Water agencies, despite the restrictions, took record amounts of water after the drought ended, according to the final numbers recorded as California’s water year ended Friday.

One of the reasons for the record-setting pumping is that much of the water this year went to refill the underground Kern Water Bank, largely controlled by billionaire farmer Stewart Resnick, and to the smaller Diamond Valley reservoir, which serves Southern California. Both reservoirs were drawn down during the three-year drought that lasted from 2007 through 2009.

In all, a record 6.5 million acre-feet was pumped from the Delta in 2011, enough to serve California’s entire population for about a year and a half, according to government figures reported by the Environmental Defense Fund.

The previous record was 6.3 million acre-feet in 2005, the year biologists concluded that the Delta was experiencing a ecosystem collapse.

The federal pumps that serve the San Joaquin Valley’s west-side farmers did not run especially hard this year, but the state pumps that send most of their water to Kern County and Southern California did.

“If you have more storage, you’re going to have more of these years when the water is available, you take it,” said John Leahigh, chief of operations planning for the State Water Project.

Most of the increased demand for Delta water since the 1990s is coming from Southern California, he said.

The conflict between water supplies and the health of the West Coast’s largest estuary exploded four years ago, when U.S. District Judge Oliver Wanger, shown evidence that Delta smelt were nearing extinction, ordered tougher limits on pumping.

The limits continue to be adjusted by regulators and court orders as they try to balance the needs of water users and fish, but a new study obtained by Bay Area News Group shows regulators have a poor understanding of how many fish — particularly salmon, steelhead and green sturgeon — the pumps kill.

“What I found was a frustrating lack of information on which to base the estimate,” said Andy Jahn, a Ukiah-based consultant and oceanographer who recently completed the study critical of how water agencies count their toll on Delta fisheries and suggests ways to improve it.

The kill of splittail, a large minnow, does not greatly worry Jahn and other biologists who say it is more a sign of a population spike in response to a wet year.

The bigger problem is that the number of salmon, steelhead and sturgeon killed at the pumps is poorly understood because state and federal water agencies do not do enough to account for less obvious ways the pumps kill fish, Jahn said.

Jahn said the estimates do not take into account such things as increased numbers of predators lurking upstream of the pumps to eat small fish caught up in the pumps’ suction.

And they don’t use modern genetics to identify the various runs of salmon, opting instead to simply classify fish based solely on their size.

Government figures show the pumps this year killed 738 Central Valley steelhead, 4,360 winter-run Chinook salmon and 52,504 spring-run Chinook salmon, according to Garwin Yip, the National Marine Fisheries Service’s branch supervisor overseeing water operations in the Delta.

But many of the fish counted as spring-run salmon, which are protected by the Endangered Species Act, were actually fall-run salmon, which are not, Yip said.

Using genetics, it would be possible to determine how many of those fish counted as spring-run were actually from that run and how many were actually from the more abundant fall run.

“They just aren’t doing what it takes to understand the damage that is caused by the exports,” Jahn said.