Chesapeake Biological Lab researcher Ed Houde and his graduate assistant Carlos Lozano (upper left) found a lot of hogchokers on a sampling cruise in the Choptank River — but that's not the fish they were looking for. Drawing of menhaden by Duane Raver. Photograph by Michael W. Fincham.

FROM THE DOCK DOWN AT THE TAIL END OF SOLOMONS ISLAND, I can watch the charter boats heading out through the early light for a day of fishing. Dozens of charter boat captains keep their boats down in this small Southern Maryland harbor near the mouth of the Patuxent River. From here they carry out clients who drive down from cities like Washington, D.C., and Baltimore, hoping to land some big fish from the Chesapeake Bay.

I'm waiting to board the RV Rachel Carson, an 81-foot, shallow-draft vessel that launched only two years ago. It is the primary research vessel for the Chesapeake Biological Laboratory, a marine science center that launched 86 years ago. Now part of the University of Maryland Center for Environmental Science (UMCES), the lab has long been known for housing a cadre of fishery scientists focused on figuring out what is happening to fish stocks in the Bay.

Seven charter boats, according to my count, are already motoring quietly past the research boat in a single-file parade. On the bridges, the shadowy figures of captains at the wheel, and down in the open cockpits, the silhouettes of men with coffee cups in hand outlined against the eastern light. Gliding out onto the broad mouth of the Patuxent River, the captains curve their boats to the east and open up their throttles. The sterns sink, the bows lift, and the boats race hard toward the open Chesapeake.

Most of those charter boats will be hunting for striped bass, the most popular target fish for recreational fishermen who pay big money and make the long drive down to this Solomons Island harbor. And the big stripers they're hunting will be hunting a small fish called menhaden.

Ed Houde will also be looking for menhaden today on this research vessel, but he's a fishery scientist who only wants to count the fish, not catch them or eat them. A compact, dark-haired man with a bushy, slightly graying moustache, he arrives at the Rachel Carson with a laptop and a search plan. It calls for a series of cruises that will seek out juvenile menhaden this summer in two Maryland rivers: the Choptank and the Patuxent. Both researchers and recreational fishermen are interested in this small, little-known fish, because they know it provides food for more famous species like striped bass, bluefish, and weakfish. Research samples from these summer cruises could help solve one of the major mysteries bothering both fishermen and scientists: Where have all the menhaden gone?

On the bridge of the Rachel Carson, Houde spreads out a chartbook on a table to review today's plan with the ship's captain, Mike Hulme, and the lab's marine superintendent, Bruce Cornwall. Today's mission is finding out whether many (or even any) young menhaden have gone up the Choptank River, a long winding river on the other side of the Bay. "We'll do the trawl just below the Dover Bridge," he tells Hulme. "We know that is a good place." Hulme nods and soon has the Rachel Carson powering across the open Chesapeake toward the Eastern Shore at 24 knots an hour, its props kicking up four separate rooster tails behind us.

It's a Bay that's changed since Houde made his first boat ride across the mainstem of the estuary. The year was 1980, and he remembers that a new governor, Harry Hughes, had just declared the Bay "a national treasure." The Chesapeake Biological Laboratory, fortunately for him, was hiring new faculty to study the estuary. He still has vivid memories of those early boat trips. "If you were out here on the Bay in July and August, you would see schools of fish everywhere, all around you these little menhaden," he says. "In the 70s and 80s, the abundance of young menhaden was very high."

Houde began work on the Chesapeake just in time to see the tail end of that great abundance, episodes when the water could suddenly seethe with a white, splashy energy as bluefish and stripers, ospreys and pelicans all attacked, setting off feeding frenzies on schools of menhaden gliding near the surface. A sheen of fish oil would soon spread on the water, and any fishermen lucky enough to be nearby would hustle over, hoping to get in on the action.

Where all that energy went is a mystery. Menhaden stocks in the Chesapeake are now at their lowest point in the past 54 years. It's a mystery that matters to recreational fishermen who claim that low levels of menhaden are starving a lot of stripers. It's a mystery that matters to a lot of commercial fishermen also. In Maryland and Virginia, pound netters catch menhaden to sell as fish bait, as do five small "snapper rig" boats that fish the southern Bay, working out of Reedville, Virginia. The town is also a base for Omega Protein, a Houston-run corporation that operates the last "fish reduction" plant on the East Coast. Menhaden may be a small, oily fish that nobody eats, but it supplies the largest commercial seafood harvest in the Chesapeake Bay.

In the 30-plus years since he arrived at the lab, Houde has become a leading authority on the early life stages of species like alewives, anchovies, herring, and menhaden. They may be less sexy and less studied than striped bass and blue crabs and oysters, the Bay's iconic species, but anchovies and menhaden are the most numerous fish in the Bay. And as forage species for other fish, they seem to play essential roles in the energy flows of the whole ecosystem.

Menhaden populations, however, have been low for 25 years, according to Houde, who says, "Overall, we don't know what has driven that." We're down in the long, narrow shipboard lab, where Houde is checking his data sheets for the day and trying to explain why menhaden populations are such a puzzle.

Pieces of the puzzle can be found hundreds of miles from here. "Menhaden spawn out on the continental shelf," explains Houde, "and later come into estuaries." It takes the right combination of ocean currents and winds, of course, to deliver menhaden into estuaries along the coast. When they deliver an especially large mass of larvae, the payoff can be a lot of new menhaden, a "year class" large enough to sustain population levels for several years. That right combination of forces, however, is almost impossible to predict, and according to some researchers, it seems to include slugs of water from warm-core rings and onshore streamers that break off from the Gulf Stream and push larvae toward the Chesapeake. One potent force recently identified is the Bermuda-Azores High, a weather pattern that correlates strongly with high recruitments of menhaden.

The number of menhaden larvae arriving at the mouth of the Chesapeake Bay can vary widely from year to year. The data above come from 18 winter cruises that sampled 5 sites from November to April at the mouth of the Chesapeake. Most of the larvae reached the Bay 30 to 60 days after they hatched. Their dominant prey at that stage of development are tiny crustaceans called copepods. Source: Carlos Lozano.

The menhaden puzzle clearly has a lot of parts, and it's the last part — what happens to larvae as they come into the Chesapeake — that Houde has focused on. To get a rough estimate of the numbers and ages of larvae entering the Bay, Houde and his graduate student, Carlos Lozano, ran cruises down near the mouth of the Bay over three winter seasons. They hit the same sites, trip after trip, month after month, dragging trawl nets through the chilly waters in hopes of catching and counting menhaden larvae at their entry point into the system. It was cold, slippery work with ice forming on the decks and rails and 400-pound nets swinging alongside the boat.

One payoff from his winter cruises has been evidence that the number of larvae coming into the Bay can vary hugely from year to year. "We found that larval ingress varied ninefold during the three years that we were out there," says Houde. The winter of 2007-08, for example, had nine times more larvae than the year before.

That payoff only raised some new puzzles. The jump in incoming larvae never showed up in later surveys of menhaden young-of-the-year. When Houde compared his record of incoming larvae with a survey of juvenile menhaden run by the Maryland Department of Natural Resources, he found no connection. Big years for menhaden larvae did not bring big years for juveniles in the department's surveys. One explanation could be a difference in survey gear. Another, more disturbing possibility: Something unhealthy was happening to all those new larvae once they got into the Bay.

By 8:24 a.m. the Rachel Carson has crossed the Bay mainstem and is cruising into the wide mouth of the Choptank River. It slides past the housetops and church towers of Cambridge, slips under the Route 50 Bridge, and begins winding upriver past marshes and woods that give glimpses of farms beyond. When the Dover Road Bridge finally blocks further passage, Hulme wheels the boat in a tight turnaround and the crew gets the net ready for the first mid-water trawl. Houde peers over the side. The river here is turbid.

How many of the winter arrivals made it up here into the Choptank? To count them, you have to catch them first, and that leads to a guessing game of sorts. "We don't know how to catch them when they are at this size," says Houde. "They are transforming into little juvenile fish. We don't know exactly where they are."

To come up with a search plan, scientists have to try thinking like a menhaden. Houde's thought is to start the trawl near the bottom, then raise it to a different depth and pull it through the water for a timed interval. Then repeat several times at several depths. If there are any juvenile menhaden in the river today, the net should find them.

Running a trawl takes teamwork as well as strategy. On the back of the deck, Houde has a crew of graduate students and lab technicians standing ready, holding the end of a long, green net. Working at the back-deck control console, Bruce Cornwall in a wide-brimmed hat talks with Hulme who's up front on the bridge lining the boat up for a downriver run.

Cornwall gives a signal of sorts, a sudden right jab in the air, and then he pushes the throttle that unwinds the net cable. Two crew members throw over the end of the net, the boat surges downriver, the net pulls away and sinks. Houde walks to the stern, steadying the net cable with his hand. Two metal slabs, the doors that hold open the net, clank across the deck and disappear into the dark water.

The haul is underway and everybody relaxes for the 20-minute run, taking in the sun on deck or grabbing a snack down below — everybody except Houde and Cornwall and the captain up on the front bridge. Houde stands by the console, clipboard in hand, making notes on the net timing, and checking his watch constantly. "The usual: two minutes at a step," he tells Cornwall. They raise the net higher in the water column, time an interval, then raise it again. If you were a menhaden, where would you be swimming?

Houde gives the signal, Cornwall reverses the throttle, the cable drum starts groaning and the net line starts winding in. Students and technicians reappear and start muscling the net up onto the deck, laying it down in layers. Houde eyeballs the clean net and realizes his sampling didn't get all the way to the bottom of the river.

The payload is at the end of the net and it's a big haul, perhaps a historic haul. Crew members pick out 17 small fish, all white perch, and then empty the rest of the catch into a green plastic tub. To the untrained eye, it looks like a sticky clump of gray-brown pasta. To Houde's eye, it's a mass of fish larvae. "All these are larval white perch and larval striped bass," he says as he and Lozano bend close and start picking through the pasta. "There must be 100,000 or more in here. It's probably the biggest catch I've ever seen."

But this biggest catch holds no juvenile menhaden, none of the menhaden that came into the Bay as larvae last winter. "The menhaden would be bigger," Houde says, "and look like juvenile fish already." They would be easy to pick out in this mass of mixed-together larvae.

The second sampling run brings a bluegill and another mass of larval white perch and striped bass. But no juvenile menhaden. The third sampling brings two adult menhaden as well as nine bay anchovies. But no juvenile menhaden. As the Rachel Carson moves downriver into saltier water, the Choptank yields plenty of perch and hogchokers, as well as several eels and toadfish — even one big, ugly (and invasive) blue catfish. But no juvenile menhaden, not at the fourth, fifth, or sixth station.

Where have all his winter menhaden gone? They may not be here yet, says Houde, sitting at the galley table, punching his laptop in search of a wireless connection. Or they may have already come in, schooled up and left the river looking for more food. If they left any stragglers behind, the mid-water trawl missed them. The guessing game goes on.

Some of those missing menhaden, it turns out, went up the Patuxent River, back on the western side of the Bay. The next day Dave Secor, a co-investigator with Houde, led a similar crew to collect samples at six stations along the Patuxent, the river that runs right by the Chesapeake Biological Lab. They found juvenile menhaden, 45 in all, most of them where you would expect them: at the three upriver, low-salinity sites. More juvenile menhaden were in the Patuxent, suggests Secor, because more menhaden food was there. On aerial surveys he had seen a major phytoplankton bloom hovering right at the mouth of the Patuxent, but he found no blooms near the Choptank.

The two rivers, at the least, highlight in crude form one clear lesson emerging from Houde's research. To find juvenile menhaden, first find the phytoplankton blooms. Strong evidence for that lesson came from a recent study by Houde and UMCES Horn Point Lab researcher Larry Harding. They compared historical data from aerial surveys with historical records showing the recruitment of juvenile menhaden into the fish population. The records revealed strong correlations between the frequency of large blooms of phytoplankton and high recruitments of juvenile menhaden. Like scientists, menhaden seem to have search strategies for finding phytoplankton blooms: They are able to sense and track down density gradients in the water created by blooms of phytoplankton and algae. With no bloom in process, the Choptank turned up empty of juvenile menhaden while the Patuxent proved well endowed with both blooms and juvenile menhaden.

Puzzled by the decline of menhaden in the Chesapeake, Ed Houde (upper left) organized searches for juvenile menhaden in two Maryland rivers, the Choptank and the Patuxent. On the first Choptank cruise, he found no juvenile menhaden but turned up plenty of bay anchovies for Jim Seuberling (lower left) to count, as well as an occasional blue crab for Jen Humphrey (lower right), and one big blue catfish for Carlos Lozano. This blue catfish is one of the first found in the river. An invasive species native to the Mississippi drainage, blue cats are widespread in the James River and have been caught in the Potomac. Sportfishermen like catching them, but scientists worry these voracious feeders (they can top 80 pounds) will disrupt food webs supporting traditional Bay species. Photographs by Michael W. Fincham.

If these two rivers have a tale to tell, it's part of a larger story about how timing and food may be driving menhaden recruitment in the Chesapeake Bay — or derailing it. This fish story is still being written by Houde and Secor and other scientists, and it may take more winter and summer cruises to complete the final chapter. But the plotlines that are emerging suggest that offshore winter weather patterns and onshore springtime runoff events are two of the lead players in a menhaden drama that may not have many happy endings.

When winter larvae first arrive at the mouth of the Chesapeake, they are entering a critical and highly vulnerable stage in their life cycle. Those menhaden larvae are not only transitioning into a new environment, moving out of the ocean into an estuary, but they are also transitioning to a new life stage. They will soon become juveniles and switch their food preference from zooplankton to phytoplankton, thanks to new comb-like gill rakers that allow them to begin filtering food out of the water. "It's a complex life cycle," says Houde. "When you have to filter feed, you would like to be in the Bay at a time when there is sufficient food."

The timing of their arrival can be key to their finding food. Menhaden larvae tend to enter the Bay between November and mid-April, according to Houde and Lozano, but for many of those months they will not find much food available. The time for rich phytoplankton food stocks is not November, not December, not January, not even February. Any early arrivals will have to survive a winter when the water is cold and the food is scarce — and most will not make it.

The late-comers, on the other hand, will soon find plenty of food. Larvae entering in March and April encounter a Bay that is warming up and a springtime runoff that is firing up plankton blooms. Blooms in April, May, and June, according to Houde and Harding, bring big jumps in menhaden recruitment because they create a lot of phytoplankton just when menhaden larvae are transitioning into filter-feeding juvenile fish.

What brings in a lot of late-arriving menhaden? A warm, dry, late-winter weather pattern, the gift of a high-pressure system that moves back and forth between Bermuda and the Azores. When a large Bermuda-Azores High shifts to the west, it creates clockwise winds that pull warm air up from the south and help drive menhaden larvae toward Atlantic Coast estuaries. It also discourages storminess that can disrupt larval migrations. When the high pressure is small or shifted toward the east, however, those winds have less effect on larval transport. That has frequently been the case during recent decades of low menhaden recruitments. The shifts and sizes of Bermuda-Azores Highs are, in turn, affected by larger, longer-lasting shifts in sea-surface temperatures called the Atlantic Multidecadal Oscillation.

The Bermuda-Azores High affects more than menhaden recruitments, according to Bob Wood, a scientist with the National Oceanic and Atmospheric Administration who first identified this effect. A former Houde student, he found that frequent favorable Bermuda-Azores Highs also help raise recruitment levels for spot and summer flounder, two other Bay species that spawn in coastal shelf waters during winter months.

Ed Houde measures one of the 9 adult menhaden found on the Choptank cruise. The Patuxent River cruise netted 45 juvenile and 280 adult menhaden. Photograph by Michael W. Fincham.

Which brings us to a paradox in the menhaden puzzle: A good year for menhaden arrivals may be a bad year for menhaden survivals. Warm, dry winter patterns created by Bermuda-Azores Highs bring more menhaden into the Bay, but cold, wet winters with high springtime runoff seem to supply the most food.

There's a second paradox. Good years for new menhaden are usually bad years for new stripers. And vice versa. Cold winters and wet springs often lead to a lot of new stripers, but they usually disrupt the influx of new menhaden. With this see-saw pattern at work, high populations of stripers will never match up for long with high populations of menhaden, their favorite food fish.

Surprisingly, this negative see-saw pattern that Wood discovered also holds true for other species: A year of high influx for shelf-spawning fish like spot and summer flounder is usually a year of low influx for other Bay-spawning fish like white perch, alewives, and blueback herrings.

So where have all the menhaden gone? There's no simple answer, but there are some emerging hypotheses, none of them very hopeful. Long-lasting trends in the Atlantic Multidecadal Oscillation have led to fewer Bermuda-Azores Highs, to fewer warm, dry, late winters, and to fewer large influxes of menhaden larvae into the Chesapeake. Those trends may be changing, but they shift slowly. Over decades.

An even less-hopeful hypothesis, according to Houde, suggests that the large-scale climate pattern called global warming may have encouraged menhaden to spawn in waters farther north from the Bay, making it less likely large numbers of larvae will make the trip down to the Chesapeake. Recent surveys show higher numbers of new menhaden arriving in estuaries north of the Bay.

For Chesapeake Bay larvae, offshore winter weather patterns seem to control their arrivals, and springtime runoff events seem to control their survivals. Global warming, offshore winter patterns, springtime runoff events — none of these forces can be controlled by changes in fishery management. But they can be mitigated or magnified.

There's no easy advice in Houde's work on how to improve menhaden recruitments into the Chesapeake. The only thing that can be controlled in the meantime is the commercial harvest, and that harvest probably does have an effect, according to Houde. "If not enough eggs are being produced now to get high recruitments," he says, "that could be a reason for the low recruitments we are seeing. It may play a role."

A cutback on commercial harvests could lead to more spawners setting more eggs and larvae adrift in the coastal ocean. Increasing spawning far out in the ocean seems a small step to take in the face of events as powerful as climate, weather, and freshwater flow. But Houde still stresses, "You want more eggs to ensure more recruits." In a boom year these extra eggs and larvae could magnify the size of a large year class. In low years, cutting back on harvest could help sustain a spawning stock until all those larger environmental forces line up.

These small steps become even more important, says Houde, just when all those large-scale forces are so out of sync. That may be the final paradox in the menhaden puzzle.