Life-giving grasses in the Chesapeake Bay have recovered from the ugly beating they took in the fall, when Hurricane Irene and Tropical Storm Lee created huge water surges that turned the water brown and threatened to blanket them with sediment.

But the surge of polluted water from the storms and a surge from heavy spring rains and snowmelt might still increase the size of the bay’s annual, oxygen-depleting dead zone next year and hasten the demise of the endangered bay oyster.

Scientists from the Virginia Institute of Marine Science who conducted aerial surveys of the bay in November said this week that grasses survived in the Susquehanna flats, where the Susquehanna River pours millions of gallons of water into the bay every minute. As feared, some along the edges of the bay were ripped out, but most held firm in the 13,000-acre flat, they found.

When the monster storms struck in late August and early September, scientists worried that the grasses that provide oxygen for marine life, food for waterfowl, and habitats for fish, oysters and a range of organisms in the nation’s largest estuary would be lost, as they were when Hurricane Agnes hit in June 1972.

Drenching rains from Lee produced the second-largest water flows from the Susquehanna into the bay since Agnes. The flows were so rapid that every gate of the Conowingo Dam in northeast Maryland was flung open, sending tons of grainy sediment and other junk that had collected behind the dam for decades pouring into the river.

Bruce Michael, director of the resource assessment service for the Maryland Department of Natural Resources, said the late-summer timing of the storm helped the grass survive. By September, the grass is mature.

“Since they are so well established, they were able to withstand this large sediment plume,” Michael said Thursday.

The bay might still have suffered other internal damage from the storms, said Beth McGee, senior scientist for the Chesapeake Bay Foundation. “The other issue that folks were concerned about was the impact from the nutrient pollution, with all that rain. That won’t be clear until next year. We might see some dead zones,” McGee said.

Dead zones are lethal events that occur when phosphorus, nitrogen and sediment pour into waters from rain runoff, feeding algae that blooms and dies rapidly and creating a thick, black goo. It’s fed on by microorganisms that suck away oxygen in deep water, suffocating bivalves, like oysters, as well as some fish and any life that can’t skitter to safety.

Nitrogen is made up of fertilizers that flow off farms and lawns. Phosphorus comes from both animal waste from farms as well as overflows of storm water and raw sewage in cities during nearly every steady rain.

Before the storms, the bay had already had one of its largest summer dead zones ever, stretching 83 miles from the Baltimore Harbor to the middle of the Potomac River region in late June.

There had also been runoff from spring rains and snowmelt, which sent major surges of fresh water into the salt- and fresh-water estuary that diluted the salinity oysters need to live. When watermen in the northern Chesapeake set out to harvest the bivalves in November, they made a grim discovery.

“They saw mortality among oysters because of all that fresh water,” McGee said. “So the positive news is the fact that the grasses were able to withstand that big of a punch. But the punch had multiple impacts. We’re still holding our breath.”