The Prince George’s County Council on Wednesday endorsed a 10-year, $1.2 billion plan to improve the county’s management of its storm-water runoff, after the state and federal government ordered communities to slow pollution flowing to the Chesapeake Bay.

The program, approved unanimously, would cost homeowners up to $62 annually in new fees and would cost businesses and religious institutions $372 per acre of paved surfaces.

The program also offers breaks to those who take steps on their own to manage storm water. Homeowners, businesses and religious institutions would get credit for installing rain gardens with special plantings that soak up water, putting out rain barrels to catch and use rain, or for planting a “green roof” to help slow and cleanse runoff.

In Prince George’s, a large shopping center such as the Boulevard at Capital Centre would pay about $12,000 per year, according to the fee schedule approved by the council. Smaller strip centers would pay about $1,000.

Religious institutions will be able to lower their costs by adding plantings and by taking steps to educate congregants about storm-water controls.

Similar programs are required in other jurisdictions that have waterways flowing into the Chesapeake, as the result of the settlement of a lawsuit brought by environmental groups.

The council, rushing to complete a packed agenda before going on a five-week recess, also confirmed new leaders for two key government departments, but the nomination for the Department of Transportation and Public Works is on hold.

The council voted unanimously to approve Haitham A. Hijazi as director of the new Department of Permits, Inspections and Enforcement and Adam Ortiz to lead the Department of Environmental Resources.

County Council Chairman Andrea Harrison (D-Springdale) announced that the nomination of Darrell B. Mobley to head the $36 million Public Works and Transportation Department had been withdrawn. Until recently, Mobley had served as Maryland’s acting transportation secretary in the administration of Gov. Martin O’Malley (D).

A top official in the administration of County Executive Rushern L. Baker III (D) said Mobley’s nomination would be resubmitted later. Mobley, who has been acting head of public works and transportation since July 3, will remain on the job, said Bradford L. Seamon, Baker’s top aide.

Harrison, who had not responded in recent days to requests for comment about her opposition to Mobley, said Wednesday that she wanted more time to see him on the job. She said that she would prefer a county resident for the post but that she knew that was not always possible.

“I am not saying he can’t do the job,” she said.

Prince George’s does not have a residency requirement, but Harrison frequently has complained about Baker nominees when they aren’t county residents. Mobley, an engineer, lives in Lutherville, north of Baltimore.

Seamon said that the Baker administration’s decision to withdraw the nomination would give the council more time to get to know Mobley, 45. “He will be the director,” Seamon predicted. Mobley is paid $175,000.

The creation of the new permitting department and the appointments of new leaders are part of a reorganization of county government that Baker promised during his 2010 campaign. His goal, he has said, is to streamline permitting and inspections procedures that have made Prince George’s legendary for red tape.

Hijazi, 54, a Syrian-born engineer whose career in Prince George’s County government has spanned 20 years, helped redesign the permitting system before being asked by Baker to head the new, $7.8 million permitting department. He previously was head of the Public Works and Transportation Department. He is paid $180,000.

Ortiz, 39, headed Baker’s CountyStat program, which uses data analysis to assess government operations, before taking over late last year as acting head of the environmental agency. The former mayor of Edmonston is paid $150,000.