This spring was another season of ups and downs for the Chesapeake’s troubled American shad as recent monitoring and stocking reports show that restoration of the once-abundant migratory fish to Bay tributaries remains an elusive goal.

Spawning shad surged to another record high in the Potomac River this spring, even as they hit record lows for the second straight year in Virginia’s largest tributaries.

To the north, the number of shad migrating up the Susquehanna River ticked up a bit after three consecutive record-low years, but remained a fraction of levels seen in the early 2000s.

Meanwhile, stocking programs attempting to bolster depressed shad runs around the Chesapeake took a hit as they were hard to find in some rivers — and hard to catch in others. Overall, juvenile stocking in Bay tributaries this year appears likely to be the lowest since major efforts began more than two decades ago to rebuild populations of the migratory fish.

Shad spend most of their lives in the ocean, but return to their native rivers to spawn. Historically, tens of millions thronged tributaries, supporting fisheries hundreds of miles upstream. For early colonial settlers, they provided a much-needed food source after hard winters. As recently as the 1950s, they were the largest commercial fishery in the Bay.

But overfishing, the construction of hydroelectric dams that blocked access to historic spawning grounds, pollution and other factors have reduced their numbers in recent decades to all-time lows in many rivers along the East Coast.

To counter that trend, utilities and states have poured tens of millions of dollars into efforts to improve fish passage past dams — and have even, in some cases, removed the dams altogether — as well as trying to bolster populations with hatchery-reared fish.

American shad catches have been banned for decades in the Bay and most places along the East Coast, and new regulations have sought to limit their “bycatch” in fisheries that target other species. This fall, the Mid-Atlantic Fishery Management Council, which regulates commercial fishing in federal waters more than three miles offshore, will consider whether to tighten the 181,000-pound limit on shad and river herring bycatch that it imposed in 2014.

The Potomac River continues to stand out among Bay tributaries — and even the East Coast — as a place where shad are rebounding. Figures from the Potomac River Fisheries Commission show this year’s shad run was a record 139.2 percent of its restoration target, which was based on population estimates from the mid-1900s. Shad numbers on the Potomac have exceeded the target for six consecutive years.

“It continues to bump up,” said Martin Gary, the commission’s executive secretary. Biologists are unclear why shad have done so much better there than elsewhere. But Gary noted that monitoring by the Maryland Department of Natural Resources has found relatively consistent strong shad reproduction in the Potomac over the last 15 years, compared with most other rivers.

Just to the south, the James and York rivers could use such help. They again saw record low shad runs, based on monitoring by the Virginia Institute of Marine Science. The Rappahannock, which a few years ago had appeared to be on its way to a solid recovery, fared only slightly better, hitting its worst mark since 1999.

“Unfortunately, we’ve got three very low indices and very few answers,” said Patrick McGrath, a VIMS marine scientist who works on the annual shad index. “We really don’t have a reason why. The weather was a little weird, but it wasn’t bad.”

On the Susquehanna River, the Bay’s largest tributary, the number of shad counted at the Conowingo Dam fish lift ticked up a bit to 14,276, an improvement after three consecutive record lows. Still, that was just 7 percent of the number that passed the lift at its peak in 2001. Biologists are hoping that the tens of millions of dollars in fish passage improvements that were committed to earlier this year by Exelon Corp., the owner of the dam, will improve the situation over time.

But getting fish to suitable spawning areas in the Susquehanna will also require better fish passages at upstream dams. Fewer than half the shad that passed Conowingo this year made it past Holtwood, the next dam upriver, and just 178 made it past all four hydroelectric dams on the lower river.

The weak fish runs — and problems catching fish on the Potomac — hampered stocking programs in many areas around the Bay. On the James River, just 1.9 million shad were stocked, well below the 4-million goal. “It was a tough year,” said Mike Odom, manager of the U.S. Fish and Wildlife Service Harrison Lake Fish Hatchery in Charles City, VA.

Fish for the hatchery come from the Pamunkey River, historically a reliable shad-producing tributary of the York River. But after several poor years, biologists are planning to give up there and try catching some next year in the Potomac River.

“It’s horrible,” said Bob Greenlee, a fisheries biologist with the Virginia Department of Game and Inland Fisheries, which supplies fish for the hatchery. “It’s been really difficult to come up with broodstock out of the Pamunkey.”

The Pamunkey Indians, who operate their own hatchery on the river, didn’t bother to start operations this year because of a lack of fish.

The Potomac is already the main source for eggs and sperm used in most other stocking efforts around the Bay. But even though its run was strong this year, biologists had a hard time getting American shad because their nets kept getting filled with gizzard shad, a species that is non-migratory — and non-edible, at least for humans. Their abundance has been growing in recent years, also for reasons unclear to experts.

When biologists did catch American shad, they were overwhelmingly of one gender, complicating breeding.

“There were plenty of American shad on the Potomac for our broodstock, but there were a lot of days where we would have tons of females, but you just didn’t catch many males,” said Chuck Stence, of the Maryland DNR anadromous fish program.

In the Choptank River, the DNR ultimately was able to stock about 2.5 million American shad, a bit below its 2.7-million goal.

Another 290,000 hatchery-reared juvenile American shad were released in the Patapsco River, reaching the target for that urban waterway, where shad stocking efforts are in their fourth year. About 615,000 hickory shad, a smaller cousin of the American shad, were also stocked in the Patapsco.

But on the Susquehanna, which also relies primarily on the Potomac for hatchery broodstock, just 1.7 million young shad were stocked, the lowest of any recent year.

The Pennsylvania Fish and Boat Commission’s Van Dyke Hatchery on the Juniata River once routinely produced 10 million to 20 million shad fry annually to stock around the Susquehanna watershed. But the eggs that drove those numbers came from fish caught in the Delaware, Hudson and other rivers. Those sources are no longer available, as their shad stocks have become depleted.

“We just try to produce as much as we can from what we get,” said Josh Tryninewski, a fisheries biologist who manages the commission’s stocking efforts.

In Delaware, biologists stocked about 448,000 shad fry in the Nanticoke River, somewhat fewer than the long-term average, said Johnny Moore, a fisheries biologist with that state’s Department of Natural Resources and Environmental Control. The state has released about 500,000 annually since its stocking effort began in 1999.

Moore said the Nanticoke River shad run appeared slightly stronger than last year, but stocking efforts were hampered by low water temperatures that reduced larvae production. Biologists use shad from the Nanticoke, and reared the eggs in a riverside hatchery.

“We had a very narrow window of optimal temperature for us, and we think that just really slowed down production,” Moore said.

No shad were stocked in the Anacostia River in the District of Columbia, where about 1 million a year are typically released, because of water problems at the district’s hatchery.

The mixed results around the Bay left the Potomac fishery commission’s Gary scratching his head. “It’s really perplexing,” he said. “Hopefully, we’ll see some progress in some of these other systems.”