Shad runs were weak for a second straight year in most Bay tributaries this spring, with shad runs on Virginia rivers hitting their lowest levels since 1998. Meanwhile, migrations on the Susquehanna continued their five-year slide.

Scientists said the poor spawning runs by the migratory fish were likely due to factors in the ocean, noting that other rivers along the East Coast also saw weaker-than-normal runs.

Biologists expect runs to eventually rebound on most rivers, but they have deep concerns about the Susquehanna—historically the largest East Coast spawning area for shad—where the spawning run has dwindled by more than two-thirds since 2001, and many worry the downward spiral could continue.

Nonetheless, there was still good news for many areas. Despite weak runs, biologists said eggs collected from returning fish were in unusually good condition.

That bolstered hatchery production and resulted in the highest stocking levels seen in Virginia. Biologists stocked nearly 16 million shad larvae, with most going into the James and Rappahannock. The Potomac and Pamunkey—the “donor” rivers for the egg-producing fish—were stocked with more than 2.5 million fish to replace those removed for restoration in other rivers. The Pamunkey and Mattaponi Indian tribes also reared several million more fish to stock in their respective rivers.

“The runs were down, but we had outstanding production with the eggs we got,” said Tom Gunter, who oversees the shad restoration program for the Virginia Department of Game and Inland Fisheries.

Maryland officials also reported a good year, stocking nearly 3 million American shad in the Patuxtent and Choptank watersheds, and another 500,000 in Marshyhope Creek, a tributary to the Nanticoke River. For the second year, the Delaware Department of Natural Resources and Environmental Control reared its own shad larvae, and stocked 513,000 in the Nanticoke and its tributaries, nearly doubling last year’s effort.

But efforts faltered in the Susquehanna, where weak egg collections, largely from the Delaware and Hudson rivers, resulted in only about 5 million shad larvae being produced—less than half of the annual goal for the river. To offset this decline, eggs were also collected—for the first time in many decades—from the Potomac River. The shad were stocked in tributaries throughout the watershed, including New York.

Shad are an anadromous fish, meaning they live most of their lives in the ocean but return to their native rivers to spawn, often swimming hundreds of miles upstream before releasing their eggs. Their springtime spawning runs once numbered in the tens of millions and often provided a source of food for frontier settlers after long winters. In the 1800s and early 1900s, shad supported one of the most valuable fisheries in the region.

In recent decades, populations in the Bay—and along much of the East Coast—hit record lows as a result of overfishing, pollution and the closure of historic spawning areas by dams and other obstacles. The sharp drop resulted in a moratorium on shad fishing since 1980 in Maryland, 1982 on the Potomac River and 1994 in Virginia. Also, the Atlantic States Marine Fisheries Commission, which manages migratory fish along the East Coast, ended shad fishing in the ocean last year.

Because they link upstream areas with the Chesapeake, shad restoration has been a priority for the Bay Program. State and federal agencies, nonprofit organizations, Native American tribes and others throughout the watershed in recent years have not only stocked hundreds of millions of shad, but worked to remove dams and build fish passages to reopen areas long closed to the migratory fish. As a result, shad populations in many rivers have been trending up, but remain at a fraction of their historic levels.

Because of the low population level, the size of the shad runs are more susceptible to the effects of year-to-year weather variations that affect migration and spawning.

That was seen this year when shad runs declined nearly everywhere. On the Potomac, home for the region’s healthiest shad stock, annual surveys captured 21.3 shad per net, slightly less than the 12-year-average of 21.5. That was down from the recent high of 39 in 2005, but considerably better than lows of 13.4 and 11.3 when the survey began.

In Virginia, the James and York rivers had the weakest shad runs since the Virginia Institute of Marine Science began annual monitoring in 1998, and the Rappahannock was below average, said John Olney, a VIMS fisheries scientist. The continuing downward trend on the York, which long had the state’s healthiest population, is particularly troubling, he said.

On the Susquehanna River, only 56,899 shad were counted at the Conowingo Dam, the first of four major hydroelectric facilities encountered by migrating fish. That was a sharp drop from the 193,574 observed in 2001.

The news was better in Maryland, where Brian Richardson, a fisheries biologist with the Maryland Department of Natural Resources, said runs on the Patuxent River appear to have increased. “I was impressed with the number of American shad we had out there, and hickory shad as well.”

The state has stocked the Patuxent since 1994, and the effort has been so successful that the percentage of hatchery-reared fish in the river has dwindled from 100 percent to 23 percent last year. “If we see that figure again this year, we’re likely to cut back,” Richardson said. “We can shift those resources to another tributary.”

Richardson said large-scale stocking has not been going on long enough in the Choptank and Nanticoke rivers to result in sizable spring runs.

Biologists said the impact of this year’s poor shad run on most rivers can be overcome if the fish that did return have good reproduction, which would fuel future population growth. Jim Cummins, of the Interstate Commission on the Potomac River Basin, said the cool spring temperatures that helped egg production for the hatcheries may bode well for natural reproduction.

“I would characterize the Potomac as having had ideal spring conditions,” Cummins said. “You can have less fish and better reproduction. I’m optimistic that will happen this year.”

But even that is murky. While egg production may be good, a recent study in Virginia suggests the survival of young shad is determined largely by river flows from late June through August. Years with high flows tend to produce more fish, while low river flows result in fewer fish.

After a dry late spring, biologists were hoping for a turnaround during the summer. “We’ve been looking at a low flow year so far,” said Alan Weaver, of the Virginia Department of Game and Inland Fisheries. “If things don’t increase, four or five years from now, the shad run might not be good again.”

All of the hatcheries in the Bay watershed treat young shad with tetracycline, which leaves a “mark” on the otolith, or ear bone, of the fish. That allows biologists to examine fish when they return to spawn and determine whether they came from the hatchery, or are “wild.” The offspring of hatchery fish do not bear the mark, and the goal of hatchery programs is for the wild offspring to eventually dominate the population—as happened on the Patuxent—ending the need for the stocking program.

It’s a huge job: Fewer than 1 percent of hatchery-reared larvae survive the four to six years it takes to mature and return to spawn. In Virginia, officials have estimated that the cost of each returning fish is about $75. “Our goal is to get out of the hatchery business,” said Gunter, of the VDGIF.

Ultimately, biologists hope to build larger, more stable populations in the rivers and—because shad can spawn more than once—have large numbers of shad of multiple ages returning each year. That would stabilize the population, and reduce the impact of poor reproduction in a single year. “If we can get to a more stable number, a few off years here and there won’t upset things too much,” Weaver said. “It will just be minor fluctuations.”

That appears to be what has happened on the Patuxent, the smallest river system stocked in the region. The hatchery effort was relatively large compared to the size of the river, allowing a booming population to develop, which—as this year showed—is more immune to annual changes than other river systems in the region.

But the reverse is happening on the Susquehanna, where the percentage of “wild” fish sampled at the Conowingo Dam has been decreasing. In 2005, just 35 percent of the fish sampled were wild, down from 71 percent in 1998.

One reason could be the discontinuation of a program that trucked tens of thousands of shad annually from Conowingo past the four dams located on the first 55 miles of the river, then released the adult fish to spawn.

That program was phased out in the late 1990s after the utilities that owned the four dams spent more than $60 million to build elevators to lift fish over three dams, and built a fish ladder at the fourth.

But those passages have never been able to move as many fish upstream as the trucks. Since 2000, when the final fish passage began operating, more than 10,000 fish have passed all of the dams just once—in 2001, when 16,200 swam past the York Haven Dam. This year, 1,913 shad made it that far; in 2004, only 219 made it.

Getting shad upstream is critical because there is no suitable spawning habitat until they pass the first three dams, and most spawning areas are beyond York Haven.

As a result, fewer fish than anticipated reach spawning areas. That lack of reproduction has been compounded by a series of problems in recent years which limited hatchery production—the 10 million larvae stocking goal for the river has been approached just once in the past five years. Most other recent years had less than half that amount.

The poor stocking, though, is overshadowed by the inability of the fish to get past the dams, said Mike Hendricks, a fisheries biologist with the Pennsylvania Fish and Boat Commission.

“At this point, fish passage is more important than what we produce in the hatchery, because unless we can improve fish passage, it’s a road to nowhere,” Hendricks said. “It doesn’t matter what we produce in the hatchery.”

Nowhere on the East Coast do migrating shad have to find their way over so many barriers. “That’s a lot to ask, we’re finding,” Hendricks said.

A bit of good news is that the owner of Holtwood Dam, PPL Corp., which has been one of the more problematic dams for shad passage, has proposed changes that could improve fish passage while increasing electricity production.

“We are really looking forward to this Holtwood redevelopment and working with Holtwood to improve fish passage,” Hendricks said. “That is going to be an important component for the future.”