Many Bay tributaries saw their weakest shad runs in years — perhaps ever — this spring as the silvery fish continues to struggle to make a comeback around the Chesapeake and along the East Coast.

Data show the James, York and Susquehanna rivers had their worst American shad spawning runs in recent history.

Biologists say the cold winter, cool spring and sudden warmup in the middle of the spawning run may have contributed to the poor spawning run.

“Catches, in general, were extremely low,” said Brian Watkins, a biologist with the Virginia Institute of Marine Science, which annually surveys the state’s major rivers. “What we kept hearing all up and down the coast was the same thing — poor. It wasn’t just a Chesapeake Bay thing.”

There were some exceptions. The shad population on the Potomac River continued its upward trajectory. And shad numbers in the adjacent Rappahannock River also showed hints of recovery.

But on the Susquehanna River — once the largest shad spawning river on the East Coast — the 8,341 shad lifted over the Conowingo Dam were the fewest since the multimillion dollar fish elevator began operating in 1997. That continued a steady decline in shad numbers since it reached a peak of 193,574 in 2001.

“It is like we are continuing to find a new bottom here,” said Josh Tryninewski, of the Pennsylvania Fish and Boat Commission’s anadromous fish restoration unit. “It is concerning to say the least.”

The James and York rivers had their lowest catch indices since 1998, when VIMS researchers began monitoring.

The preliminary James index, which estimates relative shad abundance, was 1.33 this year, well below the average of 6.4. The preliminary York index was 1.93 compared with the average of 5.74.

Neither the James nor the York have shown a significant long-term trend in the monitoring.

The story is better on the Rappahannock. Its preliminary index of 5.08 was the lowest since 2009, but still above its average of 3.83 since 1998. “The Rappahannock has been showing a glimmer of hope over the years,” Watkins said.

The best news in the Bay region continues to be in the Potomac, which has shown a steady increase in shad abundance since the late 1990s.

The river met its recovery goal in 2011, with shad returning to relative abundances not seen since the early 1950s — making it one of the few bright spots for American shad along the East Coast, where overall abundance is near an all-time low.

This year, shad abundance continued to increase, hitting 133.1 percent of the restoration target, according to data collected by the Potomac River Fisheries Commission.

It’s unclear why the Potomac has fared so well. Jim Cummins, living resources director for the Interstate Commission on the Potomac River Basin, said several factors may have contributed.

A fish passage completed 15 years ago at Little Falls Dam near the District of Columbia opened about 10 miles of the river before Great Falls forms a natural barrier to upstream migration. That area might be especially important for spawning success, Cummins said, because it has a smaller population of minnows, which are major predators of shad eggs, than downstream areas.

Also, a return of underwater grass beds in the tidal fresh areas of the river may have helped by providing a refuge for young shad, Cummins said. And water quality in the river has generally improved.

“These recoveries are not caused by one thing,” Cummins said. “It is a combination of factors.”

Whatever the reason for the comeback, Martin Gary, director of the Potomac River Fisheries Commission, said there are no plans to open the river to harvests beyond current rules that allow fishermen to keep some shad caught as bycatch in the striped bass fishery. Gary said he would like to see clearer evidence of a Baywide recovery before that happens.

“As a manager, I don’t see this as a Potomac-specific issue,” he said. “I see it more as a Bay issue.”

Neither Maryland nor Delaware have programs to assess the spring shad run.

The poor shad run in most areas, coupled with unfavorable weather, also hurt shad stocking efforts. The late spring followed by a rapid warmup provided a narrow window to catch shad, and biologists said eggs from fish caught toward the end of that period, as the water warmed, were in poor condition.

“We had such cold weather, and then it heated up real fast,” said Chuck Stence, of the Maryland Department of Natural Resources anadromous fish program. “It doesn’t give you a whole lot of time to go out and catch your broodstock.”

The number of shad larvae stocked in the Choptank was low: 635,000. But that was offset in part by good survival in ponds at the hatchery where biologists rear larger shad, which have higher survival rates when stocked. They were able to stock 456,000 early juvenile shad, which were 30–45 days old, and 38,000 late juveniles, which were about 90 days old. Both of those numbers were similar to recent years.

In Delaware, 447,000 larvae were stocked in four locations on the Nanticoke and its tributaries, a bit less than their 500,000 average, said Johnny Moore, a fisheries biologist with the Delaware Department of Natural Resources and Environmental Control’s Division of Fisheries.

Just less than 2 million were stocked in the Susquehanna by the Pennsylvania Fish and Boat Commission, the fewest of any recent year. As many as 4.7 million had been stocked in the Bay’s largest tributary as recently as 2010.

The U.S. Fish and Wildlife Service and the Virginia Department of Game and Inland Fisheries stocked 3.5 million shad larvae in the James River, fewer than the river’s 5 million target.

Things were worse for the Pamunkey Indians, whose hatchery stocked less than 300,000 larvae on the Pamunkey River, a tributary to the York. Last year, it produced more than 2.1 million.

“It took us two weeks of fishing before we started even catching any shad,” said Glen Miles, who operates the tribe’s hatchery. “My dad was one of the fishermen. He said he hadn’t seen it this bad in 40 years.”

Still, even in a generally poor year, there were splashes of good news, even for stocking efforts. This was the third, and final, year of stocking river herring on Baltimore’s Patapsco River, and biologists said it was their best for stocking the fish.

Of the two river herring species, the DNR stocked 543,000 alewife larvae and 60,000 early juveniles, as well as 200,000 blueback herring larvae and 90,000 early juveniles. It also stocked more than 1 million hickory shad and 300,000 American shad into the urban waterway.

In addition, monitoring by the U.S. Fish and Wildlife Service found evidence of natural reproduction by blueback herring this spring. “My preconceived notion of the Patapsco was that it was too impaired from storm drain runoff and all the insults that it sees,” said Steve Minkkinen, who heads the USFWS Maryland Fisheries Resource Office. “It is nice to see that some anadromous species can still survive there.”

Shad and river herring are anadromous fish that spend most of their lives swimming along the coast but return to their native rivers to spawn. Once their numbers were staggering — stories from colonial times tell of migrations so dense that fish would be crushed by wagons crossing streams. For much of the 20th century, shad supported the most valuable commercial fishery in the Bay.

Decades of overfishing, dam construction, habitat destruction and pollution have reduced their numbers to a fraction of historic levels. Efforts around the Bay have sought to rebuild populations through stocking; the removal of dams and construction of other fish passages; and improved water quality, but populations have remained low.

Fishing for American shad and river herring is banned in most areas along the East Coast, and other conservation efforts have been ramped up in recent years.

In August, the U.S. Fish and Wildlife Service filed new comments seeking greater action by Exelon Corp., owner of the Conowingo Dam, to improve fish passage at the dam. Exelon is seeking a new multi-decade operating license for the 100-foot-high Susquehanna River dam from the Federal Energy Regulatory Commission.

Efforts are also under way to curb the bycatch of shad in other fisheries along the Atlantic coast. In June, the Mid-Atlantic Fishery Council, which regulates catches in waters more than 3 miles offshore, reduced the allowable shad and river bycatch from 89 metric tons to 82 metric tons in the Atlantic mackerel fishery.