The Chesapeake Bay cleanup effort has fallen behind by almost 25 percent in reducing a key pollutant because of lagging progress in Pennsylvania and New York, federal regulators warned Friday.

The Bay cleanup plan imposed by the Environmental Protection Agency at the end of 2010 had called for 60 percent of the actions needed to restore Bay water quality to be in place by the end of next year — roughly halfway to the 2025 deadline the states had agreed upon.

Now, it appears the majority of the action to control nitrogen — the prime nutrient affecting algae growth in the Bay’s saltier water —may be left until late in the cleanup process, something officials had hoped to avoid.

“Overall, we continue to make progress, however, there are some sectors in some states where we are falling behind,” said Shawn Garvin, EPA’s Mid-Atlantic regional administrator, in releasing the agency’s latest evaluation of state efforts. “We recognize that based on actions taken to date, and the current projections, that it is unlikely that we will meet” the 2017 goals.

After analyzing progress made by each of the seven jurisdictions in the Bay watershed in 2014-15, and their expected efforts through 2017, the EPA expects Delaware, the District of Columbia, Maryland, Virginia and West Virginia will meet their interim goals for nitrogen phosphorus and sediment reductions, although not all were on pace to do that at the end of last year.

New York is expected to miss goals for all three pollutants, though, and Pennsylvania will miss the nitrogen and phosphorus goal.

EPA officials said they believed New York had adequate programs set up to ultimately get its cleanup back on track. Much more problematic is Pennsylvania, which Garvin said faces a “significant lift” to reach its goals. The state accounts for 89 percent of the 10 million-pound Baywide nitrogen shortfall projected for the end of next year.

The Bay cleanup plan, or pollution diet, called for reducing the amount of nitrogen entering the Bay annually from 260.2 million pounds in 2010 to 219.5 million pounds by 2017.

Pennsylvania officials in January announced plans to “reboot” the state’s cleanup efforts, but the EPA said what it’s seen so far is not enough to get the commonwealth back on track to meet its 2025 goals.

EPA’s review said Pennsylvania would need to place “considerably greater emphasis” on controlling runoff from agriculture, an effort that has suffered from years of underfunding and understaffing.

The agency also expressed doubt that the state could meet its stormwater goals, and suggested that some of that shortfall be shifted to other sectors, such as wastewater treatment plants, where nutrient reductions are ahead of schedule.

Federal regulators warned that when Pennsylvania develops a new strategy to guide cleanup efforts from 2018 through 2025, the agency may require state officials to provide more documentation than other states about the adequacy of their plans.

EPA officials also warned they could take a variety of other actions if greater progress is not made, such as increasing oversight of how federal grant money is spent, and expanding regulatory programs to cover smaller farm animal feeding operations.

Neil Shader, press secretary of the Pennsylvania Department of Environmental Protection, acknowledged cleanup efforts lagged from “years of inaction” that preceded the administration of Gov. Tom Wolf, but said state agencies are working with conservation districts and stakeholders to accelerate nutrient control efforts.

“Through the administration’s “reboot” strategy, we will build on these early successes and continue to identify additional pollution reduction opportunities and engage with the public to bring every possible resource to the effort,” Shader said.

But Harry Campbell, Pennsylvania executive director of the Chesapeake Bay Foundation, said the state lacked adequate funding to enact its programs. It’s “unclear,” he added, “when or if those vital resources will be made available.”

While other states were making better progress, the review offered hints of future concerns.

Much of the reductions so far have come from wastewater treatment plants, which account for about three-quarters of all nitrogen reductions since 2010. The wastewater facilities already have achieved their share of the overall nitrogen reduction goal for 2025.

But that means about 71 percent of future nitrogen reductions will need to come from agriculture, where progress has been more difficult to achieve. EPA’s review showed that through 2015, farming operations in Pennsylvania, New York, Delaware and Maryland all lagged in meeting their nitrogen reduction goals.

Nitrogen reductions from the heavily agricultural watersheds of the Susquehanna River and the Eastern Shore are essential to reducing the oxygen-starved dead zone in the upper Bay.

“We recognized from the outset that our agricultural sector is an area that we continue to need to work with,” Garvin said. He said the agency is working with the states to get programs in place to help meet the goals, find additional resources and target programs to areas that would be most effective.

Besides citing problems in Pennsylvania, the agency also downgraded its rating of Delaware’s agricultural program to “enhanced oversight” because of concerns over implementation of its permitting program for livestock operations and its nutrient management program.

In a statement, Delaware officials said they considered EPA’s evaluation “fair and objective” but expressed a “continued commitment” to reduce nitrogen from agriculture, stormwater, wastewater and septic systems.

Pennsylvania, New York and Maryland face an extra challenge as they may need to find ways to offset additional nutrients which are no longer being trapped behind Conowingo Dam, and are flowing into the Bay from the Susquehanna. As part of its review, the EPA told all three states that they need to work together to develop a strategy to achieve pollution reductions beyond those originally planned.

The state-federal Bay Program is in the midst of a multi-year review of cleanup progress. That midpoint assessment, when complete next year, is likely to show even greater pollution reduction shortfalls for all jurisdictions as it takes into account phosphorus-saturated soils, climate change, land-use changes and other issues.

While the EPA review found the region was on track overall to meet phosphorus and sediment goals, the agency warned that could change once the midpoint assessment is complete., The EPA said that “changes in levels of effort may be necessary in order to achieve the 2025 targets for all three pollutants.”

“We recognize that coming out of the midpoint assessment … things are just going to get more and more difficult, and we are committed to working together to accomplish those goals.” Garvin added.

The EPA in 2010 established a Baywide cleanup plan, known as a Total Maximum Daily Load, that established annual limits on the amount of nitrogen, phosphorus and sediment — the pollutants primarily responsible for fouling the Chesapeake ’s water quality.

Because of the failure of previous cleanup plans to meet deadlines, the EPA and states set a series of two-year goals, known as milestones, to help keep efforts on track toward the interim 2017, and ultimate 2025, goals.

Nonetheless, William Baker, the bay foundation’s president, noted that the previous two years was the third straight milestone period in which Pennsylvania missed its goals.

“It is well past time for Pennsylvania to accelerate its pollution reduction efforts, and EPA must do more to ensure that Pennsylvania obeys the law, he said.

The full reviews can be found here