A white swan flexes its wings in the shallow water in the Chesapeake Bay off Magnolia Ave. in Anne Arundel County. The annual State of the Bay report has been issued and looks at the health of the bay on January 2, 2013 in Annapolis, MD. (Jonathan Newton/THE WASHINGTON POST)

Chesapeake Bay oysters are being resurrected from the dead. Blue crabs are roaring back. And after taking a huge blow from the monster storm called Sandy, the weakened bay proved in the fall that it could right itself and come back looking fresh.

Except for a troubling decline in underwater grasses that help filter pollution and sustain marine life, many of the bay’s health indicators remained the same or improved since they were examined two years ago, according to the 2012 State of the Bay report released Wednesday by the Chesapeake Bay Foundation.

The foundation assessed the bay’s pollution levels, its habitat and its fisheries and graded it on a scale that ranged from a dismal one, which would mean it is dead, to the pie-in-the-sky 100, if it were once again the youthful, drop-dead gorgeous picture of health it was when European explorers arrived in the 1600s.

“We’ll never see that again,” said William Baker, president of the foundation, which gave the bay a grade of 32, or D plus, a slight improvement from 2010 and much better than the 28, or D minus, from 2008. “But a 50 would be great. That would mean the bay is halfway to where it was historically.”

The Chesapeake is the nation’s largest estuary, a 200-mile-long mix of fresh and salt water that supports more than 3,500 plant and animal species. Thirty-two is the highest grade the foundation has dished out since it was founded in the late 1960s. The lowest, 23, was issued in the early 1980s.

Baker, the foundation’s president, attributed the slight health improvement reflected in the 2012 report to an earlier bay cleanup plan led by states.

The report follows upbeat announcements from Virginia and Maryland that the oyster population, decimated by disease, is showing signs of a rebound. Virginia watermen harvested only 79,600 bushels of oysters in 2005 but hauled in more than 236,000 bushels in 2011. Maryland’s crop jumped from 26,400 to more than 121,000.

Blue crabs were even more robust, as the number of juvenile crabs in both states shot up from 207 million in the winter dredge survey of 2011 to more than 600 million last year. The growth followed the closing five years ago of the winter dredge fishery, in which watermen harvested mostly pregnant females with a steel dragnet, killing as many as they caught. The overall crab population grew from 250 million when dredge fishing was closed to more than 750 million last year.

A 2011 study by Johns Hopkins University and the University of Maryland Center for Environmental Science found that cleanup efforts have reduced oxygen-deprived events in the bay known as dead zones. Last year’s dead zone plague, which basically kills fish, oysters and crabs almost on contact, was the second-smallest since 1985.

That was a big deal because the 2011 one-two punch of Hurricane Irene and Tropical Storm Lee, which muddied the water with huge loads of sediment, were expected to produce some of the largest dead zones ever. But that didn’t happen.

It’s encouraging news, Baker said, but nothing to celebrate. “The bay is dangerously out of balance still. The good news is it’s headed in the right direction. The solution is exactly what’s in the bay blueprint,” he said.

By that, he meant the Environmental Protection Agency’s most aggressive plan to date to reduce pollution in the Chesapeake, a two-year-old “pollution diet.” It compels the watershed’s six states and the District to significantly reduce the amounts of nitrogen, phosphorus and sediment that flows from cities and farms into streams, creeks and rivers that feed into the bay.

Nitrogen and phosphorus cause an explosion in the growth of algae, which blooms and dies in a rapid summer cycle, sucking oxygen from the water. Sediment is basically dirt that can turn the water a muddy brown and smother bay grasses, destroying them.

Those grasses are the reason the bay failed to achieve a higher grade in the foundation’s report. In 2010 and 2011, the levels of the grasses, the bay and its rivers dropped by 20 percent. The report blamed the die-off on warmer waters and heavy rains, much of it from storms, that washed sediment into the river from as far away as New York.

Most sediment rushes downstream from the Susquehanna River’s origin in Cooperstown and collects in pools behind Maryland’s Conowingo Dam, near where the river empties into the bay at Havre de Grace.

But the pools have filled up over the decades, and more and more new sediment is sloshing over the gate. During Tropical Storm Lee, the Susquehanna’s flow was so powerful that sluice gates had to be opened, allowing record amounts of sediment to sail through.

In the four categories that comprise the bay’s habitat – including forest buffers, wetlands and resource lands that suck up storm water runoff and help stop storm surges — only underwater grasses fell dramatically in the foundation’s assessment.

The EPA and state plan seeks to reduce the amount of the bay’s yearly sediment by 20 percent, to 6.4 billion pounds, by 2025. It also seeks to limit nitrogen by 25 percent, to 185 million pounds, and reduce phosphorus by 24 percent to 12.5 million pounds.

But the EPA’s cleanup is being challenged by farmers, home builders and others who stand to bear the brunt of its costs, in the tens of billions. Water and sewer operators that must find billions of dollars to fund upgrades have complained that the timetable is too short. And environmental groups have challenged an EPA plan that allows groups such as farmers that meet pollution reduction goals to sell credits to others that do not, saying that the agency has no way of knowing whether the sellers actually reduced pollution.

The Chesapeake Bay Foundation disagrees with the challenges.

“The current bay plan is what’s going to get us to the next level,” Baker said. “I can’t tell you when it’s going to happen . . . whether it’s five years or 10 years. But we can’t stop now.”