Like a patient out of intensive care yet still suffering aches, pains and the need for a lot of rehabilitation, San Francisco Bay is on the mend but far from enjoying a clean bill of health.

That’s the conclusion of a new report released Monday by a team of scientists studying Northern California’s signature natural feature and a broad range of its issues — from wetlands to wildlife, toxic pollution to trail access.

“The bay’s health is definitely getting better. We’re making progress,” said Andrew Gunther, an environmental scientist and chief author of the “The State of San Francisco Bay 2011.” “But we still have a way to go. Starting with the Gold Rush, we had a century of degrading the bay. And we’ve only been restoring it since the early 1970s.”

The report comes out every two years in advance of the biennial State of the Estuary Conference, a scientific and public policy meeting that starts Tuesday at the downtown Oakland Marriott.

Among its key findings this year: The bay is far less polluted now than in the 1950s and 1960s. After Congress passed the Clean Water Act in 1972, billions of dollars were spent, and continue to be spent, upgrading the sewage treatment plants that filter the wastewater of 7 million Bay Area residents and release it into the bay. Modern technology removes up to 99 percent of the pollutants in that wastewater. Meanwhile, toxic substances like DDT and PCBs have been banned, no significant filling of the bay has happened in decades, and in the past two years state regulators have imposed strict new rules requiring Bay Area cities to dramatically reduce the amount of trash that flows down storm drains and creeks into bay waters.

Wetland restoration also is a major bright spot. In the past decade, roughly 10,000 acres of wetlands have been restored, much of it at the former Cargill salt ponds in the South Bay. The bay has roughly 50,000 acres of tidal marsh, up from about 40,000 in 1999, and researchers are working toward a long-term goal of 100,000 acres. Most encouraging, biologists already are seeing increases in birds, and a wide variety of fish, from anchovies to leopard sharks, are turning up in the newly restored wetlands.

But there are still major problems.

Among the top problems, according to the report, is the continued diversion of fresh water that would have naturally flowed into the bay. Large dams and pumps that move billions of gallons of water from the Sacramento-San Joaquin River Delta to farms and cities have cut freshwater flows into the bay by 50 percent. That has allowed salty water from the ocean to push farther eastward under the Golden Gate, in significant concentrations up as far as Contra Costa County.

That change, which accelerated in the past decade, has been linked to crashing fish populations, said biologist Christina Swanson, one of the report’s authors.

“For the past several decades, the bay has been in a state of chronic drought,” Swanson said. “Protecting the bay’s ecosystem and recovering its fisheries will require changes in water management in the bay’s tributary rivers and the Delta to increase freshwater flows, particularly during the spring.”

Compared to the 1980s, the abundance of pelagic, or open water, fishes in the past five years was 88 percent lower in Suisun Bay, 68 percent lower in San Pablo Bay, and 55 percent lower in South Bay, the report noted. That information comes from monthly fish surveys done in 35 locations around the bay by state Fish and Game biologists who have used nets to catch and measure fish regularly since 1980.

Other challenges include invasive species, like the overbite clam, which crowd out native species. Tougher regulations requiring ships to empty their ballast water outside the Golden Gate have made a difference, but the bay still has more than 200 nonnative species that in many cases have pushed out or diminished natives.

And there are legacy pollutants left over from the Gold Rush like mercury, which still washes down from closed mines in Santa Clara County and the Sierra Nevada. The bay is slowly flushing more mercury out to the ocean than is put in, but it will take generations before all fish in the bay are safe to eat, particularly for women of childbearing age.

The report, which will be posted at www.sfestuary.org, was prepared by the San Francisco Estuary Partnership, a program of the Association of Bay Area Governments that is funded by the U.S. Environmental Protection Agency and the state of California.

One major challenge, as state and federal agencies move ahead with restoring 15,100 acres of former Cargill salt ponds, is funding. With budgets tight, future progress may be slow going on that work, and on efforts to expand the Bay Trail, 310 miles of which is completed toward a 500-mile goal.

“San Francisco Bay is at the hub of our economy and our quality of life,” said Gunther. “How are we going to keep improving the bay? To get the benefits, we are going to have to make investments.”

Contact Paul Rogers at 408-920-5045.