A new study is in full swing to examine whether the Conowingo Dam is choking off a vital supply of natural materials needed to sustain wildlife habitat located in the lower 10 miles of the Susquehanna River and the Upper Chesapeake Bay.

Most of the concern about the dam has focused on the deluge of sediments that will head downstream when it fills. But some biologists say that not enough of certain types of sediment is getting past the dam, which hurts downstream habitats.

“A certain amount of alluvial material — whether sand, gravel, boulders or leaf litter — is a natural component of river waters and its movement downstream is a normal function,” said Larry Miller, who served as Susquehanna River coordinator for the U.S. Fish & Wildlife Service before becoming project leader at its Allegheny National Fish Hatchery.

This heavier material supports underwater grasses, protects young fish from predators and transports nutrients essential to life in the Bay, Miller said. Much of this heavy material is trapped.

Meanwhile, the river’s currents carry large amounts of fine, light sediment and pollution that compromises water quality and degrades or even destroys healthy habitats. This tends to be clay — more fine-grained and silty, often running off land as grit from building sites or topsoil from farmland.

The question for the study team is how to encourage the flow of the good materials the river carries to the Bay while curtailing the bad.

Both types of sediment have been inundating the Susquehanna for decades. Over the years, storms have exacerbated this situation, sending spikes of debris, sediment and untreated sewage into the waters. This phenomenon was evident most recently when Tropical Storm Lee sent 4 million tons of material over four days into the Bay’s usually blue-green waters, causing a cream-colored soup visible in satellite imagery.

“This type of overload can create a dead zone of oxygen-depleted water unable to support life, resulting in loss of fish, bottom-dwelling clams and worms, and other portions of the estuary’s food chain vital to the local life cycle and economy,” Miller said.

Three of the four hydroelectric dams located on the lower Susquehanna River — Holtwood, Safe Harbor and York Haven — have reached their capacity to store sediment behind their structures. The amount of fine material passing over the Conowingo Dam appears to be increasing as its reservoir approaches its storage capacity.

“It’s not ideal for the environment or for local economies when dams capture the heaviest and most natural materials while allowing the finer, more toxic sediments to get through,” Miller said. “A better balance is needed to manage this phenomenon that was once kept in check by a greener landscape and the river’s natural flows.”

Located near the mouth of the Susquehanna River in Harford County, MD, the Conowingo Dam was completed in 1928 to generate hydroelectric power for the region. River water impounded by the dam to form the Conowingo Reservoir serves as drinking water for the city of Baltimore, cooling water for the nearby Peach Bottom Nuclear Generating Station, and as a recreation destination for anglers, boaters and bird watchers.

Mark Bryer, director of The Nature Conservancy’s Chesapeake Bay Program, says that operating the dam to serve these purposes has had negative impacts for critical wildlife habitat downstream.

“As a part of this team, we hope to find ways to better balance human needs and improve downstream habitats for shad, striped bass and other key species,” he said. “That includes figuring out how to transport healthy amounts of sediment needed to rebuild lost habitats that once existed in the last 10 miles of the Susquehanna River and the Chesapeake Bay.”

That healthy habitat once warranted President Franklin Roosevelt to designate 13,000 acres of the flats as the Susquehanna National Wildlife Refuge. This was during the 1940s, when a rich, underwater carpet of wild celery, pond weeds and an array of grasses welcomed thousands of migrating waterfowl in spring and fall. The flats also harbored healthy populations of bass and welcomed one of the most impressive shad fisheries on the East Coast. Today, the refuge consists of the single, 1.5-acre Battery Island.

According to Bryer, there is hope that this situation is turning around. “We’re seeing signs that conservation efforts along the river are paying off with an incredible rebound of underwater grasses in recent years. However, there is more to be done.”

He noted that the new study is being conducted in conjunction with the Exelon Corp.’s pursuit of a new 30– to 50-year operating license for the Conowingo Dam.

The study and relicensing process is also taking place as the EPA is enforcing the Clean Water Act to require the six Bay states to establish nitrogen, phosphorus and sediment limits, or total maximum daily loads, to prevent pollution from the 64,000-square-mile watershed from reaching the Bay. Under this mandate, the states are required to reduce pollution levels by about 25 percent by 2025.

According to Claire O’Neill, project manager with the Corps’ Baltimore District, the study, expected to be completed in 2014, is in the very early stages.

Primarily funded and led by the U.S. Army Corps of Engineers, the three-year study, the Lower Susquehanna River Watershed Assessment, engages federal and state agencies and organizations such as the Susquehanna River Basin Commission and The Nature Conservancy. Members of the team meet quarterly. Meetings are open to the public.

“Through the end of summer, the focus will be on studying the sediment — how it moves through the system and its physical and chemical properties,” O’Neill said. “The team will then move on to preparing sediment transport models and eventually addressing the environmental impacts of proposed solutions.”