For years, scientists described a giant pool of sediment behind Maryland’s Conowingo Dam as a muddy boogeyman that threatened to turn the Chesapeake Bay’s blue waters into a creamy brown mess.

But state and federal experts who steward the bay have abruptly changed course, saying a two-year analysis released Thursday revealed that the sediment isn’t nearly as threatening to the bay’s water quality as first thought, and that spending as much as $3 billion to remove it isn’t worth the cost.

“Removing large amounts of sediment will not lead to any lasting improvements in water quality,” said biologist Anna Compton of the Army Corps of Engineers, which conducted the study.

She said the nutrient pollution contained in the sediment, however, is a significant threat to the bay’s health, and that a second report scheduled for the next two years will address that. She said “it’s better to focus” on managing nutrient pollution that triggers oxygen depleted “dead zones” in the bay each year.

The report was released just over a week after the election of Larry Hogan as Maryland’s next governor. Mr. Hogan, a Republican, has called for dredging behind the dam, saying it would have more impact than other expensive efforts, including storm-water fees, restrictions on farm runoff and changes in septic disposal.

“I haven’t read the report, but the Army Corps of Engineers hasn’t dredged the dam in 85 years,” Mr. Hogan said Thursday during an appearance at a diner in Dundalk, Md. “It’s a major part of the problem. So it’s the guys who have the problem and haven’t fixed the problem giving a report — so it’s probably not that fair and accurate.”

Federal and state officials undertook the newly released analysis three years ago after Tropical Storm Lee pushed millions of tons of sediment over dam’s walls on the Susquehanna River near Darlington, Md., triggering alarm from Gov. Martin O’Malley, a Democrat.

Satellite photos taken at the time showed that more than half the bay had turned brown. Some officials believed then that dredging to remove some of the sediment was a partial solution to the overflow. They believed they had time to attack the problem based on earlier studies that concluded there was enough space in the dam’s reservoirs to store sediment for at least 10 years.

But according to Thursday’s analysis, the dam already is at capacity. At the same time it showed that cloudy plumes from sediment that spills over the dam form mostly in the northern part of the bay and have little effect on marine life.

A public meeting to discuss the analysis is scheduled Dec. 9 at Hartford Community College in Hartford County, Md.

Two types of sediment flow down the 440-mile Susquehanna. One is a nasty fine particle silt that causes a cloudy plume, which blocks sunlight and kills vegetation; the other is a useful, coarse sand-like substance used by fish to lay eggs and grasses to take root.

Nutrient pollution includes nitrogen and phosphorous that originates from sewers and farms such as animal feed operations. Excessive levels of nutrients in the bay causelarge warm-weather algal blooms that trigger events that cause hypoxia, oxygen-depleted water that kills fish, crabs and anything else that can’t outrun it.

Bacteria in nutrient pollution is also a public hazard. Health officials close beaches and swimming areas in the Potomac and other rivers each time heavy rains cause sewers to overflow and wash manure and chemicals from farms.

Most sediment is harmful silt. It flows into the Chesapeake from other rivers’ tributaries, but the Susquehanna is by far the largest. Nutrient pollution attaches to sediment as they flow down river, said Mark Bryer, director of the Chesapeake Bay program for the Nature Conservancy.

About 300 million tons of sediment currently sit behind the dam. Each year, another 3 million tons arrive there, and a third of it sloshes over the sluice gates, according to the U.S. Geological Survey.

On its way to the Conowingo, sediment flows past two hydroelectric dams in Pennsylvania, Safe Harbor and Holtwood, where reservoirs are also full. Built in 1924, the Conowingo is a large dam, but it lacks the portals used by modern dams to allow sediment to more naturally flow downstream.

The report’s findings are likely to be questioned by farmers and elected officials in rural Maryland who — like Mr. Hogan — consider sediment to be a primary threat to the bay’s water quality.

“The problem with statistics is they can be used in ways that can be used for correct and incorrect positions,” said Carroll County Commissioner Richard Rothschild, a Republican and a member of the Clean Chesapeake Coalition. “In order for [the dam] to work correctly, it must be dredged.”

Mr. Rothschild said sediment that washes over the Conowingo during storms leaves a mat of sand on the bottom of the bay, killing oysters and much-needed vegetation.

“We cannot clean up the bay unless we stop the huge amount of sediment coming from storms,” he said. “Every time there’s a storm, it kills the bay from the bottom.”

Nutrient pollution, he said, is a secondary issue. But federal officials challenged that assessment.

No one is saying that sediment isn’t a threat to water quality, said Rich Batiuk, direction of the Chesapeake Bay Program Office for the federal Environmental Protection Agency.

But sediment alone “does not cause extreme problems for water quality,” he said.

The cleanup plan launched in 2010 is a “pollution diet” that compels municipalities and farms from Norfolk, Virginia to Cooperstown, N.Y., to improve water quality by upgrading water treatment facilities and place safeguards on animal feed operations to slow the flow of human and animal waste into waters. It’s set to end in 2025.

Bruce Michaels, director of resource assessment for the Maryland Department of Natural Resources, also said sediment is not as much of a concern as nutrients.

He said the Army corps analysis offered few recommendations to address sediment and nutrients. A $4 million study funded by the Conowingo’s owner, Exelon, will seek those answers over the next two years.