Nothing is going to happen right away, but within the next few years an ambitious new effort will be launched to revive the Susquehanna River’s depleted stocks of two of the Chesapeake Bay’s most storied fish.

Under an agreement announced April 25, Exelon Corp., the owner of Conowingo Dam, has pledged to take a series of steps to help American shad and river herring get past that 94-foot barrier and three other hydroelectric facilities on the Bay’s largest tributary that for decades have impeded the species’ once-legendary spawning runs.

The deal, struck with the U.S. Fish and Wildlife Service, ends a prolonged dispute over what Exelon would do to improve fish passage at the 88-year-old dam as a condition of renewing its federal license to generate electricity there for the next 50 years.

Shad and their cousins, river herring, once swam far upriver every spring to spawn, and in the 18th and 19th centuries fishermen netted them by the millions. Shad, in particular, became one of the most commercially valuable fish throughout the Bay, and was the biggest fishery in the Susquehanna.

But overfishing, pollution and the construction of dams that blocked spawning rivers took their toll. With the population depleted Baywide, Maryland imposed a fishing moratorium in 1980, which has never been lifted.

In earlier attempts to reverse the Susquehanna declines, Conowingo’s operators built lifts in 1972 and 1991 to hoist migrating fish over the dam. They seemed to work for a while, and in 2001 the number passed upriver peaked at 193,000 shad and 292,000 river herring. The tally has trended downward since, with a record low of 8,341 shad picked up last spring, and just 13 herring.

The agreement calls for Exelon to overhaul the existing east fish lift at Conowingo, going from a single 3,300-gallon hopper to boost fish over the dam to two 6,500-gallon hoppers. Other operational improvements are planned, so the capacity to move fish upriver should more than quadruple.

The Chicago-based company also agreed to work on attracting more fish to both of Conowingo’s lifts — there’s a small one on the western end — including making structural changes and altering the river flow coming from the dam.

Work won’t start until a final license is issued, perhaps by 2018, and will take about three years. But the year it gets the permit, Exelon has also pledged to begin trapping and trucking up to 100,000 shad and 100,000 river herring annually past all four dams.

The wildlife service had wanted a large new lift built on the west side of the dam, a costly undertaking that Exelon had opposed as a waste of money if fish didn’t use it. In the end, federal officials agreed to start by improving the existing east lift, as the company had proposed, with the trap-and-transport program to serve as an “insurance program” if the lift upgrades don’t work.

A new fish lift still could get built on the west side of the dam after 20 years if the upgraded east lift is not moving 85 percent of the shad and herring that reach the dam’s tailrace, or if planned downstream modifications don’t attract more fish to the dam.

And if the various projects agreed upon do not produce desired results, the 46-page pact allows the federal agency to demand adjustments.

“There is no way that today we could essentially tell them to build something that would be good for 50 years, because we may not know that right now,” said Sheila Eyler, USFWS project director. “So we need to go back and check in every few years and make sure that the fish passage is keeping up with the efficiency targets that they are required to meet.”

Fish passage improvements also have been pledged at three upstream dams. They should be in place by 2021, coinciding with the Conowingo lift upgrade.

“We are hoping that in the next five years, fish passage will really change on the Susquehanna,” Eyler said.

Exelon spokeswoman Deena O’Brien noted that the agreement avoids protracted litigation, which she called “a benefit to all parties and most importantly the American shad and river herring through more quickly realizing restoration efforts.”

The ultimate goal of wildlife agencies and conservation groups is to get a “self-sustaining population” of 2 million shad and 5 million river herring established upriver of all four dams. Because many fish will not make it that far, it means 5 million shad and 12 million herring have to get to the Conowingo tailrace.

Reaching that goal will be “a tall order,” said Genine Lipkey, a biologist with the Maryland Department of Natural Resources. An annual survey below the dam found between 140,000 and 300,000 American shad last year, she said. The state hasn’t kept similar tabs on river herring in the river.

The fish passage agreement still hinges on Exelon getting a new license from the Federal Energy Regulatory Commission. The company had earlier reached agreement on a related issue — helping American eels get upriver past the dam.

The last — and biggest — hurdle is a dispute over what, if any, responsibility Exelon bears for dealing with the buildup of nutrients and sediment in the 14-mile reservoir upriver of Conowingo. The “pond,” as it’s called, is nearly filled to capacity, an Army Corps of Engineers study found. That is allowing more of the pollutants to wash downriver into the Bay, where they complicate the cleanup of the troubled estuary.

Bay Journal editor Karl Blankenship contributed to this story.