Fishery managers stocked sharply fewer American shad around the Chesapeake this spring than in most years of the past two decades; but biologists said efforts to rebuild the shad population might be helped by a spawning run that appeared stronger than those of recent years.

Biologists attributed dismal stocking numbers on the Bay's largest tributaries, the James and Susquehanna, to high river flows and cool temperatures that hampered egg collection.

High flows also hampered fishlift operations on the Susquehanna River, where only eight fish made it past three dams to reach suitable spawning habitat - the worst year since fish passages began operating in 1997.

"It was terrible because of the high water," said Mike Hendricks, a fisheries biologist with the Pennsylvania Fish and Boat Commission.

Millions of shad once filled the Susquehanna and other Bay tributaries each spring as adults returned to their natal rivers to spawn after living for years off the East Coast. But overfishing, dams that closed historic spawning grounds to migrating fish, water pollution and other problems have decimated their numbers.

Efforts to restore shad populations in Bay tributaries have been under way for more than two decades. Fisheries have been closed, millions of larval shad are stocked each year, and fish passages have been built and dams removed to reopen historic spawning grounds.

Nonetheless, after signs of success in the late 1990s, biologists have seen little improvement over the last decade. Coastwide, American shad stocks are considered to be near an all-time low. Some say the numbers of shad caught as bycatch in ocean fisheries hinder recovery efforts, although that remains a subject of debate.

The Bay Program has a goal of stocking at least 20 million shad larvae a year, but this year's total will be a little bit more than half of that mark.

Chuck Stence, a fisheries biologist with the Maryland Department of Natural Resources, said it had been difficult to catch egg-laden shad for the hatcheries.

"The big problem is all of the debris coming down the river," Stence said. "Our nets get twisted and torn up. It's not even worth it for us to go out to lose our nets like that."

Cool temperatures that delayed the arrival of "ripe" fish ready to spawn added to the problems.

The biggest stocking shortfalls were on the Susquehanna and the James. Only 3 million larvae were stocked in the Susquehanna basin, about a fifth of the annual goal, while 2.5 million were stocked in the James - short of the 4 million that biologists had hoped for and well below the 10 million mark they consider ideal.

Things were better on the Rappahannock River where the 4 million target was hit, thanks to a late surge of ripe females on the Potomac when the broodstock was being collected. Another 500,000 were stocked in the Potomac to mitigate for those adults collected from the river. Indian tribes on the Mattaponi and Pamunkey rivers also stocked some shad in those rivers this year.

In Maryland, 1.6 million larvae and 320,000 larger juvenile shad were stocked in the Choptank this spring. In addition, up to 100,000 more juveniles - kept at hatchery ponds to reach larger sizes to help avoid predation - were to be stocked later this summer. Still, the total will be below the level of recent years.

In Delaware, biologists stocked 460,000 on the Nanticoke, just a bit below the 500,000 average for the river.

Counter to the below-average numbers of fish stocked, many biologists believe the size of this year's spawning run increased. Biologists were hoping that larvae produced by the spawning fish might have good survival, as high flows can expand nursery areas, and even make the water cloudy enough to protect them from predators.

"Usually, when we get median to high flows we get more juveniles produced," said Bob Sadzinski, a Maryland Department of Natural Resources fisheries biologist.

The exact size of the run was unclear, and the surveys to measure it were contradictory.

Surveys that used nets tended to show mediocre to poor shad runs. A gill net survey used by the Virginia Institute of Marine Science found a drop in the number of shad near the mouth of the James from last year, a similar number at the mouth of the York, and an increase at the mouth of the Rappahannock, said Eric Hilton, a VIMS fisheries scientist who oversees the survey.

On the Potomac, a gill net survey averaged only 11.7 adult shad per net this spring, compared with an average of 22 during its 16-year history, said Jim Cummins, a fisheries biologist with the Interstate Commission on the Potomac River Basin.

But he and others suggested that because of problems with nets created by high flows, those surveys underestimated the strength of this year's run.

On the Nanticoke, where biologists conduct a survey using electroshocking instead of nets, they turned up an average of 52 shad per hour, surpassing last year's record of 50, said Mike Stangl, a fisheries biologist with the Delaware Division of Fish and Wildlife. The survey has been conducted for a decade.

On the James River, electrofishing surveys below Boshers Dam in Richmond caught more shad than ever, including 130 in a single day, according to Dean Fowler, who oversees shad restoration efforts for the state Department of Game and Inland Fisheries. "Pretty much across the board in Virginia waters we had an outstanding run," he said.

And on the Rappahannock, electrofishing surveys conducted by DGIF biologists caught 59 shad above tidal waters, the most since the Embrey Dam near Fredericksburg was removed in 2004. The previous best was 12, caught two years ago, said Fowler, who also said anglers around Fredericksburg reported seeing more shad than ever.

"It was really heartening to finally see good numbers of fish show up there after all the stocking we have done," he said. "Hopefully, that is a harbinger of better things to come."

On the Susquehanna, just 20,571 American shad were lifted over the Conowingo Dam - the second worst year since a multimillion dollar elevator began carrying shad over the 100-foot-high structure in 1997 and far fewer than the record high of 193,000 in 2001.

Some biologists thought the run of fish up to the dam was stronger than that figure indicated. They said the lift missed many fish because high flows caused repeated lift closures and water spilling over the top of the dam likely lured many shad away from the device. Normally, the swiftest water flow is through the lift and the shad follow that flow into it.

"They had their lifts shut down a lot of the time during the peak of the run," Hendricks said.

The dam, located 10 miles upstream of the Bay, is the first of four major hydroelectric dams migrating shad encounter on the Chesapeake's largest tributary.

For those that made it past Conowingo, things got worse upstream.

Migrating shad don't reach suitable spawning habitat until they get past the third dam, Safe Harbor. Only eight fish made it that far - making this the worst year since the elaborate system of fish elevators began working at all three dams in 1997. The next worst year, 2008, saw 1,252 shad get past Safe Harbor.

Most of the migration stalled at the second dam on the river, Holtwood, which passed only 21 fish. High flows spilled over the top of Holtwood almost all spring, luring shad away from the fishlift. The elevator also suffered a series of malfunctions.

The owner of the dam, PPL, has launched a multimillion-dollar upgrade of the facility that includes a series of changes aimed at improving passage.

Two other dams, Conowingo and York Haven, need the Federal Energy Regulatory Commission to renew their 30-year operating permits in 2014. Biologists want improvements to fish passage to be part of the new licenses.

Among the casualties of this year's high flows were several planned studies intended to provide information about possible fish passage improvements that could be incorporated into the new licenses. Hendricks said he is hoping for better conditions so those studies can take place next spring.

"Eventually, we hope to have better fish passage out of the relicensing process," he said.