While farmers in the Choptank watershed and elsewhere are planting winter cover crops and taking other steps to curb nutrient loss from their fields, "it could be we're still seeing the [delayed] effects of just overuse of fertilizer," Phillips said.

But on the lower Eastern Shore, he added, "I don't think it's lag time. It's just too much manure being applied."

Poultry industry supporters have argued that chicken manure is not responsible for rising phosphorus levels. They note that the number of chickens raised on the Delmarva Peninsula has declined in recent years, and the birds are fed an enzyme now that reduces the amount of phosphorus in their waste.

But a recent report to the bay program concluded that phosphorus produced by the chicken flocks raised in Maryland has increased. It suggested the birds being raised are larger, producing more waste, and the waste remains in the chicken houses longer before being cleaned out, increasing the concentration.

As part of Maryland's effort to comply with the bay "pollution diet" imposed by the EPA in 2010, the O'Malley administration pledged to tighten standards on where animal manure and sludge could be spread as fertilizer. Last year, the Department of Agriculture proposed new limits, but chicken growers warned they'd be hurt by having to find other ways of disposing of their birds' waste, and farmers said they would have to pay higher costs for chemical fertilizer.

Officials withdrew the rules for revision and the regulation is on hold, pending completion of a study this summer of the economic impact. State officials have said they intend to adopt the regulation by the end of the year, though they plan to phase it in over a period of years.

In the meantime, Swanson said, the EPA has questioned whether Maryland is on track to reach its phosphorus pollution reduction target by 2017.

But Lee Currey, director of science services for the Maryland Department of the Environment, said the state is on track. While it may not reduce farm-related phosphorus as much as the EPA would like, it will more than make up for it with the completion of upgrades to Baltimore's two large sewage treatment plants.

In more developed areas, stormwater runoff is blamed for rising phosphorus levels, but it's not clear what's happening or how to fix it, Phillips said. Federal scientists are analyzing the effectiveness of stormwater pollution measures in Montgomery County, he said, and also conducting a comprehensive study in Fairfax County, Va., to try to better identify how stormwater affects streams.

"Historically, we thought the lion's share of phosphorus is washing off the landscape," said William P. Stack, deputy director of the Center for Watershed Protection. "What we've found is a large percentage of the phosphorus — as much as 50 percent — is actually originating from stream-bank sediments."

Stack said that could mean efforts to control runoff are misdirected.

"If we're really going to put a dent in phosphorus, we really have to look at stream restoration practices," he said.

Alison Prost, Maryland director of the Chesapeake Bay Foundation, said the varying condition of rivers and streams suggests that the state can't rely on reducing phosphorus overall, but needs to address "hot spots" where the nutrient's levels are not declining or even increasing.

"It shows we cannot have a one-size-fits-all approach," she said. "We need to adjust."