Will the fish come back? Will the fish make it to their spawning grounds?

These are the questions on the minds of fisheries biologists and river advocates this time of year, as they pay close attention to dam removals and other restoration efforts on streams and rivers.

Many of these restoration projects began decades ago and focused sharply on the endangered Atlantic salmon, but scientific perspective has widened to the entire complex of sea-run or diadromous fish that move between salt and fresh water, in order to restore the complete ecology of coastal watersheds.

Recently, another group of people have been watching, too: commercial fishermen, oceanographers and marine biologists who suspect that restoring populations of smaller sea-run fish like alewives and rainbow smelt will benefit ocean fish like cod.

Because large river restoration projects like those on the Penobscot and St. Croix rivers are just getting started, the true impacts on the Gulf of Maine remain to be seen.

In the meantime, the evidence in support of the theory collects.

Throughout the 19th century, citizens up and down the New England coastline protested what they saw as excessive harvest of inshore and river fisheries, and some of them mentioned linkages to the valuable cod fishery.

In his 1873 report to the U.S. Commission of Fish and Fisheries, Spencer Baird documented his conversations with fishermen about the impact of declining forage fish on groundfish populations in eastern Maine:

“That period [of large catches] was before the multiplication of mill-dams, cutting off the ascent of the alewives, shad, and salmon, especially the former. The Saint Croix River was choked in the spring with the numbers of these fish, endeavoring to ascend; and the same may be said of the Little River, the outlet of Boynton’s Lake, about seven miles above Eastport…

“The young come down from the ponds in which they are hatched, from August to October, keeping up a constant stream of the young fish. In this way a supply of alewives was to be met with throughout the greater part of the year, and nearer the coast they furnished every inducement for the cod and other ground fish to come inshore in their pursuit… the reduction in the cod and other fisheries, so as to become practically a failure, is due to the decrease off our coast in the quantity primarily of alewives and, secondarily, of shad and salmon, more than to any other cause.”

William Leavenworth, a senior research fellow at the University of Massachusetts, agrees.

“Everyone seems to have overlooked the role of the little inshore fish that few eat anymore‰ÛÓsmelt, tomcod, cunners and white perch. I think an entire inshore ecosystem has gone missing over the past century,” he said.

Salmon ate smelt. Striped bass ate young eels. Did cod eat alewives? And what are they eating now?

In a paper published in January in the journal Marine Ecology Progress Series, Theo Willis and Karen Wilson from the University of Southern Maine studied cod diets in Passamaquoddy Bay and compared their findings to similar studies in 1965 and 1896. Leavenworth and his colleague Karen Alexander are co-authors.

Cod are omnivores, or what scientists call “generalist predators.” They eat whatever they happen to come upon: scallops, crabs, urchins, herring; as a result, their diets reflect the entire ecosystem.

Cod ate more fish in 1965 than in either 1896 or 2005. As explanation, the study authors posit that the fish that cod would rather eat were already on the decline in 1896: river fisheries had long passed their peak and the smoked herring and sardine industries were taking billions of Atlantic herring out of the bay. So the cod ate more crabs, shrimp and urchins.

Then, in the decades between 1910 and 1965, scallop dragging, pollution and green crab predation on clams had taken their toll on bottom dwellers, leaving the cod with a surface diet of shrimp, krill and fish, including a few herring. By the 21st century, cod were few and far between in Passamaquoddy Bay; the 19 fish that the researchers were able to catch didn’t have any herring in their stomachs.

“What we see today, throughout the Gulf of Maine, are historic lows in forage fish abundance that have resulted in a virtual fish desert in near-shore areas, where fish were caught in abundance just a century before,” Willis and his colleagues wrote in their paper. “Restoring alewives, menhaden, and Atlantic herring may be essential in bringing back coastal cod populations and rebuilding complexity in an impoverished ecosystem,” they concluded.

As many as 32 million alewives once swam through Passamaquoddy Bay. Menhaden haven’t made an appearance in 150 years, and the region’s iconic herring weirs have been fallow for more than a decade.

Today, the system is dominated by invertebrates—animals without backbones, with less protein and nutrients than bony fish. This is why fisheries scientists have been saying that in order to get the big fish back into coastal waters, we have to get the little fish back.

Heather Deese holds a doctorate in oceanography and is the Island Institute’s vice-president of programs. Catherine Schmitt is communications coordinator for Maine Sea Grant.