The Chesapeake Bay and its rivers have lost 44 percent of their underwater grasses over the past three years, scientists reported Thursday, reducing vital habitat for crabs and fish to a level not seen in nearly three decades.

Scientists blamed weather and storms for much of the decline seen last year, but they said an as-yet unexplained long-term decline in the bay's water clarity has played havoc with this key indicator of the Chesapeake’s health.

An aerial survey flown from late spring to early fall last year found 48,191 acres of submerged vegetation, down 21 percent from the extent of grasses seen in 2011, according to scientists from Maryland and Virginia.

It was the third straight year of reported declines, following a 21 percent drop in 2011 and a 7 percent dip in 2010. Since hitting a peak of sorts in 2009, the bay's grasses have shrunk to a level last seen in 1986, shortly after scientists began conducting annual surveys of the bay's grasses.

Scientists attributed the losses in large part to an extended run of unfavorable weather, with extreme summer heat in 2010 killing off lower bay grasses and heavy rains and tropical storms knocking back vegetation in the upper and middle bays.  Hurricane Irene and Tropical Storm Lee flushed millions of tons of sediment down the Susquehanna and other rivers, turning the bay murky brown for months afterward.

Bob Orth, coordinator of the aerial survey with the Virginia Institute of Marine Science said that bay grasses "are not doing very well in the Chesapeake Bay, which is unfortunate .. given the role they play as a water quality indicator."

Between the summer heat, wet weather and storm-flushed pulses of sediment, Orth added, "the Bay’s grass beds face an uphill challenge.”

Vital shelter and food sources for fish, crabs and other animals such as turtles and waterfowl, underwater grasses have long been considered a key to the health of the bay. They need sunlight to grow and thrive, just as lawns do. Submerged plants die back, though, when the bay's waters become clouded by sediment and algae blooms, which are fed by nutrient pollution.

While underwater grass losses in previous years had been limited to just part of the bay, last year saw widespread diebacks, said Lee Karrh, a biologist with Maryland's Department of Natural Resources. He suggested that a gradual decline in the variety of grasses seen in the bay the past 30 years has made the estuary's underwater prairies more vulnerable to the vagaries of weather.

Karrh and Orth also said that in addition to storms muddying the bay, there's been an general decline in water clarity since about 1999, which has experts baffled.

"The picture is anything but clear," Karrh said. "We know there’s less light available, we’re not sure why." 

Orth said that when he goes to swim or dive in the bay, "it looks clear, (but) when you get in it looks like a fog." 

One theory is that a surge in microscopic plankton may be clouding the water, they said, but that's not been confirmed or explained.

Whatever the cause, Orth said worsening light penetration of the water has limited underwater grasses to shallower areas, where temperature-sensitive eel grass in particular is more vulnerable to extreme summer heat.

 Amid the generally gloomy news, scientists said there were two areas of the bay where underwater grasses had fared relatively well.  While tropical storm flooding damaged the large Susquehanna Flats grass bed near the top of the bay, a dense growth of vegetation survived.  Grasses actually increased in Virginia's James River.

Nick DiPasquale, director of the Environmental Protection Agency's Chesapeake Bay Program office in Annapolis, said in a statement released with the survey results that he was encouraged by those few signs of what he called "resilience" in the bay's grass beds.  But he acknowledged the "worrisome" survey results offered a "sobering reminder of how imperative it is to continue our restoration efforts.”

For more on the bay's grasses, including an interactive map, go here.