The Chesapeake Bay is seen in Chesapeake Beach, Md., in this file photo. (Ray K. Saunders/The Washington Post)

With the health of the country’s largest estuary largely unchanged over the past two years, environmentalists trying to clean up the Chesapeake Bay said they hope to work with Maryland Gov.-elect Larry Hogan (R) to improve the bay and an ecological system that is “dangerously out of balance.”

In its 2014 State of the Bay Report, which was released Monday, the Chesapeake Bay Foundation found that the bay’s water quality has improved slightly but that the gains were offset by declines in the blue crab and rockfish populations.

“While we can celebrate water-quality improvements, we must acknowledge that many local rivers, streams and the Chesapeake Bay are still polluted,” said William C. Baker, president of the foundation. “We continue to have polluted water, risks to human health and lost jobs — at huge societal costs.”

The biennial report evaluates 13 measurements in three categories: pollution, habitat and fisheries. It gave the bay a score of 32, or a D-plus — the same it got two years ago.

The Chesapeake’s score has improved since Gov. Martin O’Malley (D) took office — but only slightly. The foundation gave the bay a score of 28, or a D-minus, in 2008.

“We’re not happy about the score, but we’re glad to see that it’s going in the right direction,” Baker said.

Baker said a major cause of pollution in the bay is an excess of phosphorus. That is largely due, he added, to tons of manure — much of it from chickens — that pollute creeks across the Eastern Shore, which has a large poultry industry.

“The message is absolutely clear: Agriculture as a sector must do more. Agriculture is the largest sector of pollution coming into the bay, and fortunately it is the least expensive to control,” Baker said. “We need to get serious about controlling phosphorus.” He added that the Eastern Shore is the only part of the state where “our elected officials have continued to resist sound science by delaying new regulations to control chicken manure.”

Before O’Malley leaves office this month, he plans to enact regulations intended to curb pollution from farms. Hogan has previously described the proposed rules as a “last-minute fulfillment of a political promise to a special-interest group.”

A Hogan spokesman said in an e-mail that it’s time for a new approach. The study released Monday “is just the latest to conclude that the current strategy for restoring and protecting our greatest natural asset and America’s largest estuary is not working,” Adam Dubitsky said. He said Maryland farmers are well ahead of state and federal phosphorus, nitrogen and sediment reductions goals, while their counterparts in Pennsylvania and New York have yet to act in any meaningful way.

Baker said water-quality indicators have improved by 10 percent since 2012. Dissolved oxygen and water clarity were responsible for the increase.

The biggest declines were in fisheries, with the blue crab population dropping from 765 million to 297 million. The report said the number of adult female crabs dropped below the level considered depleted and forced states to cut back on catches to improve the chances of good reproduction.

Rockfish are also down, but the number of oysters is up in Maryland. The bay-wide catch nearly hit 1 million bushels in the 2013-2014 season, the first time that benchmark has been approached since 1987, according to the report.

Baker said members of the foundation look forward to working with Hogan to improve the bay and hope he will see the economic benefit it would bring to the state.

Baker said that when he meets with Hogan, he plans to ask him to “embrace and implement” the Chesapeake Clean Water Blueprint, which was established in 2010. It calls for a reduction in pollution to creeks, rivers and the bay and has been agreed upon by state and federal agencies and local governments.

The report says the bay region is not on track to meet the blueprint’s goal, which calls on state and local governments to achieve specific reductions.

“The Clean Water Blueprint is in place and working, but there are danger signs ahead,” Baker said. “We would urge [Hogan] to look at that, understand it and go after it with every element of his administration.”