Just off Conimicut Point in Warwick, R.I., Heather Kinney navigated The Nature Conservancy’s 21-foot workboat to a buoy marking the location of an unbaited fish trap she had set in 14 feet of water four days previously. About the size of a lobster pot, the trap was deployed as part of a research project to document the abundance, diversity, and size of the fish that spend at least part of the year in upper Narragansett Bay.

When Kinney, the conservancy’s coastal restoration science technician, and colleague Tim Mooney pulled in the trap, it contained three black sea bass, two feisty blue crabs, and an oyster toadfish — an ugly golden creature with brown stripes and spots that can survive in poor water quality. True to its name, the toadfish even croaks.

“The sea bass have dorsal spines and the toadfish will bite, so there’s plenty to be careful of when you’re handling them,” Kinney warned, as she and Mooney removed the fish and measured them before returning them to the water.

As Kinney zigzagged back and forth across the upper bay to the 12 trap sites between Rocky Point and Watchemocket Cove in East Providence, she and Mooney repeated the process of pulling in traps and setting new ones. The results were usually similar to their first haul, though at several sites they also used eel traps that targeted smaller fish and often captured dozens of juvenile black sea bass and scup. One trap contained more than 20 spider crabs.

“When the Narragansett Bay Commission reduced the nitrogen output of its wastewater plants by 50 percent, there was no record of how that affected the fish population,” Kinney said. “There was anecdotal evidence that more fish were coming into the area, but no one was quantifying it. So that’s what we’re doing. We want to see what the juvenile fish population is up here. As pollution goes down, we wanted to have a sense for how the populations have changed.”

With funding from the federal Sport Fish Restoration Program and assistance from the Rhode Island Department of Environmental Management, the conservancy’s fish survey began in 2015 using fine seine nets at 12 locations from Conimicut Point to the Pawtucket boat ramp on the Seekonk River. Two years later, the fish trap survey was added. Both surveys are conducted monthly from May to October.

“I don’t think anyone was expecting to find many fish in the Seekonk River, so everyone is surprised at the number of fish we get there,” Kinney said. “The diversity of species is surprising.”

Because the net mesh is smaller, the seine nets catch the most fish — sometimes thousands of menhaden and silversides, plus summer and winter flounder, pipefish, pufferfish, needlefish, killifish, mummichogs, striped bass, and hogchockers. Where rivers flow into the bay, they often catch freshwater species such as largemouth bass, perch, mullet, bluegill, and sunfish.

The abundance of black sea bass in all of the traps is notable, according to Kinney, because it may be a signal of the changing climate. Black sea bass, which prefer warmer waters, were seldom caught in significant numbers in Narragansett Bay until relatively recently. But, she said, most of the fish are in the upper bay because water quality has improved.

“We’ve reduced nutrients and improved water quality, but now we’re seeing how much of the story now is about habitat loss,” Mooney said. “Water quality is better but shoreline habitat is lacking in a lot of places. Fish are returning but the habitat they’re finding isn’t great.”

To learn more about habitat loss, the conservancy is conducting a video survey of the bottom of Narragansett Bay using a camera attached to a sled that is towed behind a boat. Funded by Rhode Island Sea Grant, the project will identify seafloor habitat in the region — is it muddy, rocky, sandy, or cobble? — the marine invertebrates that live there, and the general health of the habitat. The results of the video survey will help to identify priority areas for habitat restoration.

The first fish habitat restoration project will take place in the waters off Sabin Point in East Providence beginning later this month, when large concrete “reef balls” will be placed just offshore.

“The purpose of the reef balls is to test whether the structures are an effective strategy for increasing juvenile fish survival rates and increasing overall productivity,” Mooney said. “By attracting adult fish, it should also enhance recreational fishing opportunities.”

The fish trap surveys will continue for another three to five years, while the seine surveys have no scheduled end date.

“These surveys are critically important to understanding the changes taking place in our fish communities,” Kinney said.

Rhode Island resident and author Todd McLeish runs a wildlife blog.