Diver Todd Florey, who spends three or four days a week cleaning yachts in San Francisco Bay, has noticed a different mix of marine creatures gumming up the bottoms of boats since the end of the drought. He sees more mussels, for example, and fewer sea squirts.

Florey’s 45-minute plunges into the murky water, aided by a 150-foot air line, put him in a unique position to dwell on the bay’s dark underworld. But scientists say he’s observing part of a far-reaching shakeup in the 550-square-mile estuary.

A recent study by researchers in Tiburon suggests that the diverse array of plants and animals that cling to boats and docks in San Francisco Bay, often referred to as the fouling community, is reshaped by blasts of fresh water surging toward the ocean in wet times — like those that busted the five-year dry spell last winter.

The same mountain runoff and bulging rivers that boost California’s water supplies inundate the bay, providing an ecological cleanse even as some worry about too much precious water being lost out the Golden Gate.

At the root of the changes is salt. Many of the critters that thrive off high saline levels, including invasive species, can’t handle the drop in salinity, giving an edge to other marine life, the researchers said. In some spots, creatures native to the bay, such as oysters, may benefit from the reduced competition.

“The year before, we had all this stuff that looked like tumbleweed,” said Florey, who runs Hop to It Diving & Yacht Maintenance and has been scraping fouling organisms off boats in the North Bay for eight years. “But a lot of the animals just disappeared. Mussels seem to have taken over.”

While most of the affected animals are small and uncelebrated, from barnacles to sponges to tube worms, scientists say the change has broader implications. Fish and birds have different things to feed on, local ports see new organisms creating drag on oceangoing vessels, and aquaculture facilities face the possibility of new pests.

“There are a number of issues that come up,” said Andrew Chang, lead author of the study published last month in the journal Global Change Biology and an ecologist at the Smithsonian Environmental Research Center’s marine program in Tiburon.

Chang and his colleagues have been tracking life in the bay since 2001 by dangling plastic collection panels off docks. In the new study, the team went beyond looking at how temperature and season affect various organisms to evaluate the less-studied impact of wet and dry years.

They found that rainy winters, including 2005-06 and 2010-11, were among the most consequential. Some invasive plants and animals, which have come to rule San Francisco Bay after lengthy voyages in the ballast water of ships, were nearly abolished.

Critters that can’t withdraw into shells or tubes to escape rising freshwater levels, such as sea squirts and bryozoans, also called sea moss, were most vulnerable, according to the study.

The new study did not document what happened after the extraordinarily wet 2016-17 winter, but Chang suspects the same.

“Before the floods, so to speak, you could walk along the docks or the waterfront and see these large assemblages of organisms all over the place,” he said. “After the flood, there was almost nothing on the docks because it got killed off. It rotted and smelled awful for a while, but over time, things started to come back. And it was different.”

Perhaps the most significant losses were suffered by the Asian sea squirt, Ciona robusta, a notoriously problematic species in the bay and around the world. The tube-shaped, translucent invader dominated over most other bay creatures during the dry years, even posing a threat of migrating to places like Tomales Bay where it could wreak havoc on oyster farming, Chang said.

The invertebrate, however, can’t survive without significant salt levels, and its die-off presents a chance for other organisms to re-emerge.

“If you’re a manager interested in managing invasive species, you could look at this as an opportunity,” Chang said. “We’ve wiped out the community that was here before. Now you have a clean slate. It’s time to take aggressive management action.”

The study suggests that policies long pushed by environmental groups could be particularly effective after wet years, such as tightening regulations on the shipping industry, limiting the introduction of invasive plants and animals through ballast water, and restoring conditions more favorable to indigenous organisms.

Chang’s study noted that climate change could lead to an uptick in extremely wet years, meaning more chances to help the struggling natives.

Ted Grosholz, an estuarine ecologist at UC Davis who was not involved with the study, said water managers could cite this phenomenon while arguing for the release of more fresh water from dammed rivers and creeks into San Francisco Bay.

Because the estuary is a worldwide hub of trade and has become home to so many nonnative creatures, Grosholz said, the native community needs all the help it can get.

“Invasive species tend to outcompete and sometimes consume the native species that form the bottom of the food web,” he said. “These invasions have had significant impact over time.”

Along the shores of Richmond, where Chang and his fellow researchers did a lot of their work, evidence of the outsiders is clear.

“Over the years, the character of the growth has often changed from one year to the next,” said Steve Orosz, harbormaster at the Marina Bay Yacht Harbor, who is familiar with Chang’s study. “I was always thinking: Is the water warmer or colder? But I can see now how the salinity is making a difference.”

Kurtis Alexander is a San Francisco Chronicle staff writer. Email: kalexander@sfchronicle.com Twitter: @kurtisalexander