At the Conowingo Hydroelectric Dam in northeast Maryland, the barbarians are at the sluice gates.

Sediment, millions of tons of it, has flowed down the 440-mile Susquehanna River for more than 80 years and massed at the dam. And now a reservoir built to hold it is filling up.

The threat to the Chesapeake Bay came into sharp focus when Tropical Storm Lee produced record flows in the river in September, forcing officials to open the gates. Four million tons of sediment rushed through in about four days, equal to what the bay normally gets in four years. Half the bay’s blue-green waters appear as beige as coffee with cream in recent satellite images.

Worried state and federal officials are confronted with an obvious question. Could the next monster storm force even greater amounts of sediment into the bay? That could turn dirtied waters into periodic oxygen-depleted killing fields for species of marine life they are fighting to save.

Maryland Gov. Martin O’Malley (D) and Col. David E. Anderson, commander of the U.S. Army Corps of Engineers’ Baltimore District, recently launched a $1.4 million, three-year series of studies to examine how storms can undermine efforts to protect the bay from sediment and other pollution.

The District, Virginia, Maryland and four other states in the Chesapeake Bay watershed are in the first stage of an ambitious federal bay-restoration program that will cost tens of billions of dollars before it is completed in 2025.

“Tropical Storm Lee provided a vivid demonstration of the need to take steps to head off what could be a catastrophic event causing . . . enormous damage to our restoration processes,” O’Malley said. “The time to address this threat is now.”

Sediment doesn’t threaten the walls of the dam. But when Lee’s relentless rain produced near-record river flows last month, the Conowingo couldn’t stand much more water pressure. Throwing open the gates resulted in a jailbreak for the sediment.

According to a U.S. Geological Survey estimate, more than 160 million tons of sediment floats behind the Conowingo, built near Darlington, Md., in 1928. About 3 million tons arrive there each year, and about a million tons of that sloshes over the gates, said Mike Langland, a USGS hydrologist.

Environmentalists say the sediment dump during the storm was so high that it could spawn another mammoth, oxygen-depleted “dead zone” like this past summer’s.

If the storage capacity is reached in about 20 years, as Langland predicted, at least 3 million tons of sediment would wash into the bay yearly, making matters far worse.

Mixed with the sediment are large amounts of phosphorus and nitrogen from farms and cities upstream. Those nutrients are enemies No. 1 and 2 of environmentalists hoping to reduce pollution in the Chesapeake, the nation’s largest estuary.

The Susquehanna starts at Cooperstown, N.Y., flowing at about 20 miles per day in summer through Pennsylvania until it reaches Havre de Grace, Md. There it pours 18 million gallons of water per minute into the Chesapeake. It’s the biggest freshwater flow into the bay by far, supplying as much as 60 percent of the Bay’s fresh water compared with the Potomac River’s 19 percent.

The flow of sediment into the bay from the Susquehanna would increase by at least 150 percent if the dam’s reservoir filled.

On top of that, phosphorus levels would increase by 40 percent and nitrogen by 2 percent.

Not all sediment is bad. Some is composed of gravelly material that helps support bay grasses that protect young fish from predators.

But a lot of it is granular stuff that blots out light and smothers grasses in the Chesapeake. Nutrients such as nitrogen and phosphorus feed algae blooms that suck out oxygen, suffocating endangered bay oysters and other slow-moving shellfish.

“Anything that moves upstream eventually finds its way to the Conowingo,” said Mark Bryer, director of the Chesapeake Bay program for the Nature Conservancy. “Since we’ve been building dams, sediment has been a problem.”

The study is tasked with finding a way around the problem, getting sediment downriver in the least harmful way. “You don’t want it coming down in one big punch,” Bryer said.

Having a filter like the Conowingo helps, said Bruce Michael, director of resource assessment for Maryland’s Department of Natural Resources. “There’s a benefit to that dam being there” corraling it, Michael said. “We’re all trying to see how we can extend that trapping capacity behind the dam.”

Serena McClain, a director of river restoration for the conservation group American Rivers, had a different view. “Rivers move sediment. That’s their job,” she said. “When you put a dam in the river, that’s going to trap sediment. It’s only going to trap so much sediment before it goes over and is released.”

American Rivers advocates removing some dams, McClain said. The sediment the dams collect is often grit that pours through the orange mesh fencing of home builders or comes from mud loosened by bathing cattle. The Susquehanna is fed by 49,000 miles of rivers, streams, creeks, brooks and runs.

“There’s no obstruction to stop” it from being injected into the Susquehanna’s veins, McClain said.

With the help of the Nature Conservancy and other partners, state and federal officials will try to determine whether conservation measures such as cover crops, stream buffers and other methods can become an obstruction, soaking up rain before it can push sediment into waters, Michael said.

Some of those same measures are similar to what the federal Environmental Protection Agency calls for in its controversial “pollution diet” to reduce harmful sediment, phosphorus and nutrients that pour into the bay from cities and farms.

Environmentalists support stronger conservation measures, but farm lobbies and housing developers have fiercely contested these efforts, saying they’re expensive and extreme.

An American Farmers Association lawsuit against the EPA is making its way through a federal court in Pennsylvania, with support from home builders.

The federal government is putting up more than $1 million for the sediment study, according to the announcement. The remainder is being split by the Maryland departments of the Environment and Natural Resources, the Susquehanna River Basin Commission and the Nature Conservancy.

“We have to somehow defuse the impact of the time bomb that’s been waiting for the next big flow,” Bryer said.