This year's American shad run was more of the same for most rivers around the Chesapeake region: frustration and disappointment about the inability to rebuild large populations of the migratory fish.

Shad runs this spring ticked up a bit on the Susquehanna, Nanticoke and James rivers; dipped a bit on the Rappahannock; and seemed little changed in most other places. On the Patuxent River, though, Maryland officials decided to halt shad restoration after another year of poor returns.

Bringing back shad populations has been a priority for many states, as well as the Chesapeake Bay Program, and since the early 1990s, tens of millions of dollars have been poured into hatchery-based stocking programs, fish passage construction and dam removals.

Populations initially increased from rock-bottom levels of the early 1990s, when some spawning runs were so low that a few biologists thought shad might warrant endangered species protection. At that point, biologists could hardly find any fish on the James, and they were gone altogether from the Choptank and Patuxent rivers.

But over the last decade, initial signs of recovery have waned and population trends in most rivers have flat-lined or declined.

"Whatever we've been doing hasn't been working, and it's not like we haven't spent a lot of money and a lot of effort," said Greg Garman, director of Virginia Commonwealth University's Center for Environmental Studies.

A decade ago, biologists were optimistic they would see the shad population increase exponentially. In 1999, with hatchery programs boosting the James River population, a passage was built at Boshers Dam in Richmond to open nontidal portions of the river that the dam had closed to migrating shad for more than a century.

"Everyone thought after 10 years, we would be seeing at least 10,000 American shad using the fishway," said Alan Weaver, fish passage coordinator for the Virginia Department of Game and Inland Fisheries. "It just didn't seem that far out of reach."

But in its best year, 2002, about 1,000 American shad made it past the dam. Its annual average is about 200, although tens of thousands of other fish use it.

Surveys by the Virginia Institute of Marine Science show that the initial signs of recovery have halted. The river's shad population over the last decade has had no clear trend.

"As biologists working on restoration, we want to see scads of shad," Weaver said. "But it seems like they're up and down from year to year. It does get frustrating."

Likewise, when 193,574 shad were lifted over the Conowingo Dam on the Susquehanna in 2001, biologists thought their goal of getting 2 million annually past it and three other upstream dams by 2025 was within reach. Instead, shad numbers at Conowingo dropped sharply, and no more than 16,000 ever made it past all four dams-and that was 2001.

This year, the Conowingo fish lift hoisted 37,757 American shad over the 100-foot dam. That was an improvement over the last three years, but still the fourth worst since the fish lift started operating in 1997.

After surveys found no signs of shad, Maryland began stocking the Patuxent River in 1994, and the Choptank in 1996. After initial success, fisheries biologists began noticing signs of trouble in 2006. This year, they pulled the plug on stocking in the Patuxent, which was performing much more poorly than expected, to consolidate efforts in the Choptank.

"We are going to continue monitoring the Patuxent to see what is happening there," said Brian Richardson, who oversees the stocking program for the Maryland Department of Natural Resources. "But we thought we could have a much better impact on the Choptank, which is showing some positive trends."

The Chesapeake region is not unique. A 2007 stock assessment by the Atlantic States Marine Fisheries Commission, a panel of state and federal fishery managers responsible for managing migratory fish along the East Coast, declared that the coastwide shad population was "currently at all-time lows."

Theories about what's hindering the shad recovery abound. Shad are an anadromous fish, meaning they live most of their lives in the ocean but begin returning to their native rivers to spawn when they are 4- to 5-years-old, often swimming hundreds of miles upstream before releasing their eggs.

Because problems appear to be coastwide rather than focused on individual river spawning stocks, many believe shad are being impacted as they migrate along the coast, where stocks from many rivers are believed to merge. Some believe increased predation by fish such as striped bass-which studies have shown is a problem on the Connecticut River-is to blame. Others point to offshore fisheries in federal waters, where anecdotal information suggests significant numbers of shad may be caught. Still others think that subtle changes in ocean temperatures or currents might be playing a role, noting that other coastal species are also in decline.

Despite centuries of exploitation, scientists know surprisingly little about what happens to shad after they migrate out of rivers where they spawn.

"It's frustrating because there are so many variables involved," Garman said. "Where they spend most of their life is a black box. We don't really know what is going on and have even less management control over the adult period of their life history."

Shad have struggled with a host of problems over the last century. They were overfished, and dams shut off spawning runs from huge stretches of rivers. The 444-mile Susquehanna River once held the most shad spawning habitat on the East Coast. Now fish can barely get 10 miles upstream before butting up against a dam. Water quality and spawning locations in many rivers were also degraded. Also, shad have to swim through a gantlet of nonnative predators such as blue catfish during migration.

Dave Secor, a scientist with the University of Maryland Center for Environmental Science who studies anadromous fish, said the basic problem is that shad populations are very low and have lost important diversity-genetic and otherwise-so they may have a more difficult time bouncing back from any problem, whether it is predation, fishing or even several years of poor spawning conditions caused by the weather.

"As diversity is lost, shad populations adopt singular behaviors, possibly using a smaller set of habitats than those available to them," Secor said. "This in turn makes them less resilient to future stresses-they've essentially put all of their eggs in one basket."

It is difficult for people today to comprehend the magnitude of the shad decline. Their spring spawning runs in some rivers numbered in the tens of millions. Because they swam far upstream, they were often important for settlers because they arrived early in the spring, providing food after long and sometimes difficult winters.

The Potomac was filled with shad, and shad fisheries, including one owned by George Washington at Mount Vernon. In the 1830s, catches on the Potomac River reached as high as 22.5 million fish. It was not uncommon for fishermen to snare 4,000 shad in a single seine net.

The shad harvest, generally conducted in rivers to target fish on their spawning runs, was the most important commercial fishery in the Bay in the early 1900s. As recently as the 1950s, annual harvests in Bay tributaries totaled about 4 million pounds.

But the remaining populations took a hit from Hurricane Agnes in 1972. Maryland banned Bay shad fishing in 1980, the Potomac was closed in 1982, and Virginia closed its portion of the Bay in 1994.

Individual states and the Bay Program made shad restoration a priority over the years, in part because the shad's historic long-range journeys up major rivers uniquely tied upstream areas to the Chesapeake. Recreational anglers prize the fish for its fighting ability.

Stocking programs began on the Susquehanna in the 1970s, and by the 1990s, stocking efforts were under way in most major Bay tributaries. The construction of fish passages-including multimillion dollar elevators on the Susquehanna-was accelerated to help the fish access historic spawning areas. From 2000 to 2005, the Atlantic States Marine Fisheries Commission, a multistate agency that regulates migratory fish, phased out what was thought to be the last major fishing impediment to recovery, the ocean "intercept" fishery that gill-netted shad as they swam along the coast.

Nonetheless, surveys by the Virginia Institute of Marine Science since 1998 have shown no significant population trends on the James and Rappahannock rivers and a decline in the York River system. "We are continuing a trend of not showing a recovery," said Eric Hilton, a VIMS fisheries scientist. "From historical data, the stocks are still down-way down."

For years, the Potomac's shad population has been rebounding and is the healthiest of any Bay river. But that rebound has slowed in the past five years, according to the river's lead shad biologist, Jim Cummins, with the Interstate Commission on the Potomac River Basin. "We had a decent run in 2010," Cummins said. "Shad were all healthy, with more large, older shad, an observation shared by veteran anglers near Chain Bridge in the District of Columbia. But the current recovery trend is rising less steeply than it was five years ago."

Unlike other major rivers, Potomac shad are not hampered by numerous dams. Its water quality has greatly improved since the 1960s and 1970s.

So Cummins, like others, points his finger at ocean fisheries, which are suspected of catching shad when targeting species such as Atlantic herring which, among other things, is widely used for lobster bait. "When I see people eating lobster," he said, "I see them chewing up shad that should have returned to the rivers, but never had a chance to get back."

One place that has seen an uptick in recent years is the Nanticoke River, where stocking programs didn't begin until 2000. In fact, biologists on the river this spring reported the highest catch rates since surveys began a decade ago, said Mike Stangl, a fisheries biologist with the state Division of Fish and Wildlife. "I think we are seeing a trend," Stangl said, though he cautioned that counts remained far below historic numbers.

Another disappointment has been the failure of fish passages such as those at Boshers and Conowingo dams to move significant numbers of fish upstream.

Even on the Rappahannock River, where in 2004 engineers blew up the Embrey Dam, creating the only free-flowing waterway connecting the Bay with the mountains, shad have been slow to take advantage. Biologists saw American shad up to 28 miles beyond the dam site in 2008, but most years they've only spotted shad a few miles beyond where the dam stood, and the numbers have been small.

"On one hand, it is good news that we know that they've used the habitat that has been opened," Weaver said, "but on the other hand we can't really see that it's getting used much."

Scientists believe the spawning stock of each river is genetically unique, and it is also likely that there were slight variations in fish, which spawned in different reaches of those rivers. It's possible that the remaining fish do not have as much drive to get upstream as in the past, Secor said. In fact, some recent research suggests that migratory fish rely on older "leader fish" as guides. For many areas, those fish are long gone. "You have this potentially good spawning habitat, but it's lost to the population," Secor said.

While everyone agrees that shad restoration has been more problematic and taken longer than expected, none are ready to throw in the towel.

This year, hatcheries around the watershed continued to churn out millions of shad larvae to go into rivers. In Pennsylvania, 4.9 million-the most in years-went into the Susquehanna. Virginia stocked about 8 million, mostly split between the Rappahannock and James, with about 500,000 going into the Potomac. Maryland biologists were expecting about 4 million American shad to go into the Choptank, and Delaware stocked 565,000 in the Nanticoke.

A recent federal strategy for the Chesapeake Bay continued to identify American shad restoration as a priority.

And new efforts are in the works. The ASMFC earlier this year amended its shad management plan, which would close the few remaining shad fisheries in rivers along the coast by 2013 unless states can show they are sustainable. It also required states to do a better job monitoring shad, including the amount caught in the bycatch of other fisheries.

On the Susquehanna, home to the largest potential spawning grounds on the East Coast, representatives from state and federal agencies and from nonprofit organizations are pressing for better fish passages at dams to be part of new relicensing agreements that are now being developed by the Federal Energy Regulatory Commission for three of the four dams on the lower river.

"We'd like to see 75 percent efficiency at each of the lifts," said Mike Hendricks, of the Pennsylvania Fish and Boat Commission.

Right now, even if fish are lifted over the Conowingo Dam, few find their way past the next three they encounter. Because the licenses are good for 30 years, Hendricks said it's essential to get passage improvements in the 2014 license renewals.

Improvements are under way at the other facility, Holtwood Dam, which is not up for relicensing.

With some help, Hendricks said shad may still be capable of surprising people with a comeback, noting that the nearby Delaware River inexplicably had its strongest shad run in two decades this year. "Shad are contrary in every way," Hendricks said. "Trust me. I've been rearing them for 25 years."