WELLFLEET — Every spring, river herring known as alewives migrate from the open ocean up Cape Cod’s streams to ponds to lay their eggs. There, their young develop before swimming downstream in the fall to return to the sea.

The spring herring “runs” used to be big business on Cape Cod. In the 19th century, the right to fish streams was auctioned to the highest bidder, and the revenue from that sale would help fund town governments and local schools, according to biologist Barbara Brennessel. The runs were also culturally important to the Wampanoag and Nauset peoples long before European colonists arrived.

Now it’s a big deal for volunteers who stand at the edges of the streams to count fish as they swim upriver to spawn. They do their tallying in 10-minute intervals throughout the count days, says Henry Lind, president of the Eastham Conservation Foundation, which organizes the herring count in Eastham.

The Outer Cape’s count days are fast approaching — counting will begin April 1, with sampling continuing through June 30.

Brennessel, author of The Alewives’ Tale: The Life History and Ecology of River Herring in the Northeast, coordinates the Wellfleet count.

Cape Cod’s river herring population has been declining since the end of the 19th century, and the species has never recovered. By the 1960s, herring populations had fallen to as little as one percent of their historic size, according to a report in Oceanus, a publication of the Woods Hole Oceanographic Institution.

Although there’s hope that herring populations will improve on the Outer Cape as restoration continues on the Herring River in Wellfleet and new herring spawning grounds have opened in Eastham, the numbers for 2023 weren’t very encouraging.

Most counts last year were higher than they had been the year before, said Jo Ann Muramoto, the director of science programs at the Association to Preserve Cape Cod, which coordinates the volunteer counts across the Cape. But the herring’s numbers were still low compared to what they have been historically.

In the 2005-2006 season, after continued and precipitous declines, a three-year herring harvesting moratorium was enacted in Massachusetts. The moratorium was extended indefinitely when the herring failed to rebound.

The Outer Cape’s three herring counts are relatively recent in the context of the fish population’s long decline. The count on Wellfleet’s Herring River began in 2009, and those on Eastham’s Herring River and Herring Brook began in 2014 and 2016, respectively.

Last year, the two Eastham counts were close to their averages: Herring Brook had a run of 1,769 (the average there has been around 1,300) and Herring River had 3,476 (the average is 4,700). Both counts were slightly higher than in 2022, which is a good sign, but nothing too remarkable, Muramoto said. “It’s a slight improvement on a very low number,” she said.

The Herring River in Wellfleet, meanwhile, had its largest run since the count began, with an estimated 65,529 herring swimming upriver.

But both Muramoto and Brennessel felt that number was not necessarily indicative of an upward trend. Brennessel noted that the river had similar numbers in 2014 before a downswing. “It’s like a roller coaster,” she said. “It goes up for two or three years and then goes all the way down.”

For a variety of reasons, herring numbers have not changed radically since the fishing moratorium was put in place. One of the most important is offshore harvesting — the oceangoing Atlantic herring are legal to catch and often form schools with the river herring, so fishing vessels seeking the saltwater fish will often capture their freshwater relatives, too, Muramoto said.

As they migrate to their spawning ponds, herring face other key challenges: dams, gates, and other water-control structures. At these chokepoints, they end up stuck in large schools waiting for their turn to progress, making them especially vulnerable to predators. “It’s like a traffic jam,” Muramoto said.

Groundwater use and droughts also can lower river levels, making it difficult for adult herring to reach the ponds and for juveniles to return to the ocean. Brennessel described one especially bad drought during which herring were “flopping on the banks of the river.”

At the ponds themselves, water quality matters. Nutrient runoff creates algal blooms, and when that algae dies and is consumed by bacteria it uses up dissolved oxygen, resulting in hypoxia — a layer of deep water with no oxygen in it.

“There’s places in these ponds these fish can’t occupy anymore,” said Brad Chase, Diadromous Fisheries Project Leader for the Mass. Div. of Marine Fisheries (DMF). And because warmer waters can hold less dissolved oxygen, this problem is likely to grow worse as climate change makes the ponds warmer.

Still, there are signs that recovery of herring stocks is possible.

In Eastham this winter, Cape Cod Mosquito Control opened a channel between Great Pond and Deborah Pond, Chase said, which had the accidental outcome of allowing herring in the Herring Brook run to reach that pond again. DMF plans to work with the town of Eastham this summer to expand that channel and install a water-control structure. It will also be cutting out a root ball in a culvert between Deborah and Depot ponds, allowing herring to travel even farther upriver.

“We would expect it to be a good place to have fish spawn,” Chase said, and he hopes that these new spawning grounds will help the population recover.

Removing obstructions has had demonstrated benefits for herring populations. In 2010, a four-foot-wide culvert along Stony Brook in Brewster was replaced with one that was 18 feet wide. The change turned a 25,000-fish run into a 250,000-fish run, APCC data show.

The Herring River in Wellfleet could support hundreds of thousands of herring, too, Muramoto said. She believes that by widening culverts and restoring water flow, as was done at Stony Brook, the Herring River Restoration Project could raise numbers there by as much as a factor of 10.

Water quality protections like development buffer zones around wetlands, stricter septic requirements, and, in the long term, building sewer systems can make a difference, said Chase: “We just have to bite the bullet as a community and do as much as we can.”