A rescue operation led by the Marin County Fire Department hauled in 54 kayakers stranded on Tomales Bay beaches Saturday night, following dramatic wind shifts and high tides that surprised kayakers during a bioluminescence tour, a highly popular night tour where microorganisms emit phosphorescent glows on moonless nights.

No one was hospitalized, though two kayakers were treated for mild hypothermia. 

At around 8:30 p.m., a calm evening suddenly shifted to winds gusting up to 30 miles per hour, switching from northwest to south and drawing kayakers toward the bay’s dangerous mouth. The mercurial winds also slammed against an incoming tide, creating bigger waves that were breaking fast.

The wind change was unusual and caught the large kayaking groups off-guard, said Jimmy Evans, a guide for Point Reyes Outdoors. Professionally trained guides for the company fought against the surging tides and wind to tow kayakers to Pelican Point, inaccessible from the road, and Hog Island. There, the guides treated some with hypothermia kits.

Emergency crews were already attending to a capsized boat, unaffiliated with any company, when they learned the kayakers needed help. The fire department deployed inflatable rafts and jet skis to sweep up the distressed kayakers and ferried them safely to Nick’s Cove. Everyone was off the water by 1 a.m. on Sunday.

Mr. Evans said that many people over the past few days had thanked him and the other guides for saving their lives. Every sort of natural twist on the water that could have happened that night, he said, happened.

“When you’re out at night on the water, forces of nature can change quickly,” he said. “When that happens, we have to be prepared.”

Blue Waters Kayaking, in Marshall, likewise had tour groups on the water Saturday. But according to the company’s founder, John Granatir, it evacuated its groups from the water before rescue crews arrived. He noted Blue Waters is the only company with shore-side facilities, which helped his guides return kayakers without rescue assistance by 10:30 p.m. The company—which took out 42 kayakers that night—made the call around 8:15 p.m. to bring the groups back, Mr. Granatir said.

Also on the water that night was Marin County Supervisor Steve Kinsey, out paddling with his son and friends when the winds whipped up. They returned unaided. In an email, he questioned the weather forecast data local companies rely on to plan their tours.

Laurie Manarik, the owner of Point Reyes Outdoors, admitted the company may not be receiving as clear forecasts as possible. The company has relied on reports from the National Oceanic and Atmospheric Administration and a web-based service called iWindsurf to predict weather. Ms. Manarik said that the groups had been returning to the launch point at Nick’s Cove when the winds shifted three times unexpectedly and that, at the time, they had no way to predict the sudden change.

“When we launched, it was perfectly calm,” she said. “There was no forecast that it was going to peak at any time. We never would have gone out if it had been.”

She did add, however, that the company could have benefited from having more guides per kayakers out that night. Her company had eight kayakers per guide compared to the three-one ratio Mr. Granatir said his company had.

Demand for the popular bioluminescence tours has spiked in recent years, crowding traffic on the bay from both companies and private paddlers.

“They’re beautiful tours,” Ms. Manarik said. “Now we’re all gun shy again.”