San Francisco Bay is cleaner than it has been in generations, but increased pumping of freshwater to Central Valley farms threatens to turn parts of the bay into salty, fishless backwaters, according to a comprehensive report to be released today.

"The State of San Francisco Bay," which draws on two years of research, offers a primarily positive snapshot of the bay, from pelicans to plankton. The waterways that sustain and define the region feature more wetlands and less toxins and raw sewage, and are mostly safe to swim in, according to the report.

"As we move more levers, the bay does respond," said Andrew Gunther, lead author of the report, which was published by the San Francisco Estuary Partnership and heavily funded by the U.S. Environmental Protection Agency. "We can never go back to how the bay was in the early 1800s, but it's pretty clear we're making it a lot better than it was."

Things were not so rosy in the 1940s and 1950s. Developers wanted to fill in much of the bay for houses, and the water smelled so bad from discharges of wastewater and untreated sewage that it was dubbed "Lake Limburger." In Alviso, silver coins would turn brown just from toxic gases, according to the report.

Wetlands successes

Among the biggest improvements since then, the report said, is the transformation of 16,000 acres of salt flats into tidal wetlands, mostly in the South Bay. Wetlands provide homes for nesting and migrating birds, nurseries for fish, and a degree of flood control for the shoreline.

Last week, work crews breached a levee along the Hayward shoreline, allowing bay waters to flow through a 630-acre expanse of salt for the first time in 150 years.

Another highlight of the report is the reduction of metals that were once prevalent in the bay. The amount of copper and nickel, for example, dropped by nearly 50 percent from 1995 to 2010 thanks to tightened restrictions on water treatment and industrial discharge.

Residents who live near the bay have also made a difference in its health, the report concluded. Urban water use dropped 20 percent over the past 25 years, even though the Bay Area's population has grown by 20 percent. Meanwhile, record numbers of volunteers help pick up trash and remove nonnative plants.

But the report also contains warnings about the bay's future.

Populations of many fish and crustaceans - such as striped bass, bay shrimp, split-tail minnows and long-fin smelt - have plummeted with increased pumping of freshwater from the Sacramento-San Joaquin River Delta to the Central Valley, said report co-author Tina Swanson of the National Resources Defense Council.

"The further upstream you go, the less healthy the bay gets," she said. "We're essentially subjecting the bay to chronic drought conditions, even in wet years."

Dozens of species in San Pablo and Suisun bays rely on a mix of salt water and freshwater, particularly a flush of snowmelt in the spring that signals them to breed or migrate.

Lowest level on record

The amount of freshwater that flowed into the bay from September 2009 to September 2010 was the lowest level on record, continuing a 50-year downward trend, said co-author Peter Vorster of the Bay Institute. More than 40 percent of the freshwater headed into the delta was piped elsewhere before it reached the bay, he said.

"The delta is oversubscribed," he said.

Vorster noted that Central Valley farmers aren't the only ones to blame, as Bay Area residents and industries also rely on diversions of freshwater. Still, farmers need to cut back water use - just as Bay Area residents have - for the sake of the bay, he said.

Some Central Valley agriculture districts "are just swimming in water, even in dry years," he said.

Farm group responds

Fights over agricultural water use have roiled state politics for decades. Told of the report on the health of the bay, a spokeswoman for the Westlands Water District in Fresno, the largest agriculture district in the United States, said cutting such water supplies would lead to other problems.

The less water for farms, the fewer jobs and less revenue for the state's economy, said the spokeswoman, Gayle Holman. Farms in the Westlands district contributed $1 billion to the economy last year, she said.

Westlands farmers are already using less water, she said. Last year the U.S. Bureau of Reclamation allowed them 80 percent of what they had been entitled to according to their water rights, she said.

"Every drop of water our farmers use goes directly into producing food and fiber for our nation," she said. "For us, reports like this are very frustrating because we already are cutting back."

Protecting the brand

But the health of the bay has many other economic impacts, according to the report. Fisheries, tourism, property values and overall quality of life are linked to the vitality of the waterways, said Gunther, who directs the Center for Ecosystem Management and Restoration.

Without freshwater, the bay would cease to be an estuary, he said. It would just be an inlet of the Pacific.

"We are, after all, the 'Bay' Area," he said. "It's part of our identity. It's our global brand."