Some environmental groups and county officials have begun positioning themselves to challenge any new license agreement for the operation of the Conowingo Dam.

This June, the Clean Chesapeake Coalition, a group of Maryland counties which has expressed concern that increased pollution from the dam could overwhelm their Bay cleanup efforts, filed a motion with the Federal Energy Regulatory Commission to intervene in the relicensing.

In July, a coalition of environmental groups, including the Stewards of the Lower Susquehanna, the Lower Susquehanna Riverkeeper and Waterkeepers Chesapeake, which includes riverkeepers around the Bay, also filed a motion with FERC to intervene. The Chesapeake Bay Foundation, the largest environmental group in the region, filed a motion in August.

The motions allow the groups to formally comment on any proposed license submitted to FERC, and also give them the ability to challenge any final license in federal court.

The 30-year license the dam is now operating under is due to expire Sept. 1, 2014. State and federal officials have been negotiating with Exelon Corp., which owns the dam, over environmental conditions to be included as part of any new license. The goal is to agree on conditions this fall and submit them to FERC for inclusion in the new license.

Exelon is seeking a new license to operate the dam for 46 years.

Among the issues being dealt with in the relicensing negotiations is improved passage for migratory fish, the impact of fluctuating water flows from the dam on downstream habitats and species, and river access.

But the most vexing issue is what to do about the sediment that has been accumulating behind the dam since it was built in 1928. During large storms, huge amounts of the stored sediment, along with phosphorus bound to the sediment, is flushed from behind the dam into the Bay which is 10 miles downstream.

In the Bay, the sediment clouds the water, blocking sunlight needed by underwater grass beds, and can smother oyster reefs and other habitats. The phosphorus can contribute to algae blooms.

Because the dam has nearly reached is storage capacity for sediment, a recent study suggested that smaller storms are beginning to wash increased amounts of sediment downstream. That threatens the ability of states to reach Bay water quality goals.

The issue has no easy fix, and past studies have suggested solutions such as dredging sediment from behind the dam could cost tens of millions of dollars a year. Another study seeking to find a solution is under way.

A group of Maryland counties represented by the Clean Chesapeake Coalition has expressed concern that their efforts to reduce nutrient and sediment pollution to the Bay will be undercut unless something is done to prevent increased sediment and nutrients from escaping the dam.

“Unmanageable amounts of nutrients and sediments are being scoured from the Conowingo reservoir and flushed into the Upper Bay during storm events,” said Ron Fithian, a Kent Count Commission and chairman of the coalitions executive committee. He said local cleanup plans required for counties “will be difficult to justify and Maryland’s Bay restoration efforts will continue to be undermined if this single largest source of pollution is not addressed during FERC relicensing.”

The environmental groups also stressed the need to find a solution to the sediment problem. Michael Helfrich, the Lower Susquehanna Riverkeeper, said the “unnatural amounts” of sediment that can be released downstream during major storms because they have been allowed to build up behind the dam for decades “are damaging the Bay, and making the work of cleaning up the Bay even more difficult. Solutions to this, and other impacts, must be addressed in the relicensing process.”