New surveys this summer of the Sacramento-San Joaquin Delta's tiny smelt show the fish remains close to extinction, prompting questions about whether cutbacks in water pumping to protect the species did any good.

The Delta smelt population this summer fell back to the historic low set in 2005, and is now well below high points recorded in the late 1970s.

Controversial new federal rules this year reduced water diversions from the Delta on behalf of the fish. That hurt the region's farm business, which was already struggling with another year of drought.

Many observers had hoped pumping cutbacks would help the Delta smelt rebound.

But the latest population data, obtained by The Bee on Wednesday, suggest that one single action, in just one year, doesn't save a species.

The smelt's continuing plight is a reminder the Delta faces bigger problems that may have already harmed the region's economy and could eventually harm human health.

Commercial salmon fishing is closed for the second consecutive year in California and most of Oregon, partly because salmon also struggle to survive in the Delta. The estuary's water quality problems, aggravated by urban and farm pollution, are seen in toxic algae blooms and may one day make its waters unsafe.

"We've had four years of (water) cutbacks and they don't seem to be having the desired effect," said Laura King-Moon, assistant general manager of the State Water Contractors, a nonprofit association of 27 public agencies that purchase water from the State Water Project. "I think it suggests we need to have something that's more comprehensive, that does address all the stressors."

Water diversions from the Delta were cut by about 10 percent this year to protect smelt, as required by new federal endangered species rules.

The drought had a bigger effect, cutting deliveries by about 30 percent.

In normal years Delta diversions irrigate about 2 million acres of California farmland and provide a portion of the drinking water to about 23 million Californians.

The Delta smelt population has historically declined during drought periods, so another decline this year isn't necessarily surprising.

Tina Swanson, executive director of The Bay Institute, said a broader set of fixes for the Delta is essential.

She said federal rules that require cutbacks in water diversions to protect smelt were never intended to drive a rebound in the species. The rules are meant to prevent extinction, and Swanson said they're working.

Swanson's nonprofit was one of several environmental and fishing groups that sued water agencies in federal court. Their victory resulted in a ruling that brought about the pumping limits.

"It's an indication that overall conditions in the Delta remain really bad," Swanson said of the smelt count. "It's going to take years to recover this species. We need to improve the amount of water flowing through the Delta at the right times, and we need to increase the quality of that water."

The state Department of Fish and Game has been tracking smelt populations since 1959, towing a net at a fixed speed at the same locations. The number of smelt collected in each tow, averaged across the estuary, produces a population index number.

This method is used because it's impossible to count every tiny smelt in the Delta.

This summer's index of 0.3 is so low that measuring change from year to year becomes difficult, said Randall Baxter, a senior fisheries biologist at the department. The index has been below 1 since 2005, the same year it set the historic low, also 0.3.

"There are very few Delta smelt out there," said Baxter.

The results haven't been published on the Fish and Game Web site yet because the department had a problem with sampling gear during the survey period.

The repair may have slightly altered the survey, until it was detected and fixed, but not enough to significantly alter the results, Baxter said. Figuring out how to explain this accurately delayed posting of the results, he said.

A comprehensive fix for the Delta's problems is being prepared by the Bay Delta Conservation Plan. A draft is expected early next year.

The Legislature also plans a comprehensive fix in the form of new water laws. Bill language has not emerged as part of a special legislative session now under way.

Call The Bee's Matt Weiser, (916) 321-1264.