People visiting Chicken Ranch Beach at very low tide recently might have spotted curious materials floating on the surface: bright green ribbons attached to wire mesh and a  plastic bottle containing the message “research, leave alone.” If you passed by and wondered what it was, you are not alone.

“When I’m out there, people do ask me what it is,” said Hali Rederer, a master’s candidate with a focus on marine ecology in the biological sciences department at California State University, Sacramento.

The materials in the water off Chicken Ranch are part of Ms. Rederer’s thesis project, a two-year investigation into the spawning habits of Pacific herring in Tomales Bay and, in particular, the substrates they prefer to lay their eggs on.

Pacific herring are relatively small fish, typically around 12 inches long, that live in large schools from Baja California to Alaska in the eastern Pacific Ocean. The populations in California have been lower than average in recent years, but they are not endangered. 

The idea for the project arose from Ms. Rederer’s interest in abundance. As a keystone species in the food web, Pacific herring (including their eggs) are “basically eaten by everything,” as she put it: birds, seals, other fish, porpoises and more. To sustain so much sea life, the herring are typically characterized by huge numbers. 

“Personally, I’ve always been interested in biological patterns of abundance,” she said.

She was familiar with the area through her participation in citizen science projects on Point Reyes and heard from other scientists that Tomales Bay is relatively underutilized for research. It also helped that San Francisco and Tomales Bays are home to the largest herring spawning events on the California coast, according to the state Department of Fish and Wildlife, with spawning occurring roughly half of every year, from October to March.

Tomales Bay once supported a sizable commercial herring industry, though it was always smaller than San Francisco Bay’s. Pacific herring in California are caught primarily for their eggs, or roe, which are popular in Japan; most of the meat ends up in pet or animal food. 

According to records kept by Fish and Wildlife, in some years, fishermen in Tomales Bay caught a couple hundred tons of herring. But the commercial catch eventually plummeted, in large part due to falling prices for herring. 

Commercial fishing stopped in Crescent City and Humboldt Bay, two other areas that supported herring spawning, in 2002 and 2005. After the 2006–2007 season, the Tomales Bay fishery effectively ended. 

Although it is technically still allowed—with a 350-ton annual limit still in place—San Francisco Bay is the last place in the state that still attracts commercial herring vessels.

In the last annual report on Tomales Bay’s herring season, Fish and Wildlife reported that most spawning occurred around Marconi Cove, Shallow Beach and Tomasini Point, primarily on eelgrass and seaweed. The agency noted that “numerous anecdotes were given of herring ‘swimming through nets’” because they were undersized, potentially because of warm ocean temperatures and food scarcity. 

In fact, the commercial hearing fishery in San Francisco Bay closed during the 2009-2010 season because of a population crash. Ryan Bartling, an environmental scientist with Fish and Wildlife, said that, as with most pelagic species, there can be a lot of variation in densities from year to year. He could not speak to the current spawning season, but the last three seasons have seen lower than average populations in San Francisco Bay, likely due to warm water conditions that can affect food sources and “inhibit larval success.”

The end of Tomales Bay’s commercial fishery spelled the end of the agency’s monitoring of herring in the bay, which used to involve estimates of fish size and surveys of spawning. 

California is now in the midst of creating a management plan for the herring fishery, instigated by a 2012 state policy mandating better protections for forage fish. Mr. Bartling said the draft plan is expected to go to the Fish and Game Commission in October. 

The new plan will, among other things, update regulations, develop new protocols for setting catch limits, create rules for recreational herring fishing and “develop collaborative research opportunities to monitor and assess herring populations in Tomales Bay, Humboldt Bay and Crescent City Harbor,” according to the agency’s website. Theoretically, such monitoring would involve collecting information about age, size, sex ratios and spawning.

Mr. Bartling said the agency is involved in some collaborative pilot efforts in San Francisco and Humboldt Bays. But those partnerships depend on fishermen willing to donate their time to collecting information.

For now, others are putting their own spin on herring research in Tomales Bay. For instance, Audubon Canyon Ranch is studying the connection between herring runs in the bay and water bird abundance. The research was spurred by the state’s forage fish policy and the organization hopes it will inform the herring management plan. 

The nonprofit is looking at three main subjects: the impacts, over years, of herring activity on water bird populations; the effect of herring activity on foraging; and the amount of energy that herring provide water birds. “[A]lthough waterbirds are widely known to consume herring and herring roe…their potential dependence on herring remains unknown,” the group wrote in a 2016 paper. 

For her thesis, Ms. Rederer chose three sites along the western side of Tomales Bay to study 100-square-centimeter quadrants in which she counts herring roe on different substrates: eelgrass, artificial eelgrass, rocky substrate and sandy bottoms.

Eelgrass is a critical component for sea life, providing habitat and food for many animals. But the correlation between eelgrass beds and herring is complicated. 

Ms. Rederer pointed out that in 2001, when the bay’s eelgrass population suffered, herring actually thrived. “So my interest was, is [eelgrass] a preference that herring actually have?” 

In other words, in the presence of other resources, will herring spawn indiscriminately, or are there certain substrates it will prefer?

This winter is the second season of Ms. Rederer’s research. She could not yet report on this season’s spawning patterns, but last year’s preliminary results offer some clues. She said the herring seemed to prefer spawning on eelgrass, preferring true eelgrass to rocky substrate and the fake eelgrass. 

“I was surprised to see the extent of the preference,” Ms. Rederer said. Even in areas with sparse amounts of eelgrass, she would find those few strands covered in jellylike eggs.

So what could her research lead to? Perhaps that is one of the toughest things for Ms. Rederer to explain. Her project is basic science; it does not have a clearly defined application. It is possible, she said, that it could inform conversations around herring spawning, particularly if their preferred substrates are being affected in some way. 

But at the end of the day, it can be difficult for her to answer people who ask, what is this good for? There is “not necessarily a hard reason or purpose,” she said. “That is why it is basic research.”