The hydrogen fuel cells used to power buildings and a few eco-conscious cars spew no exhaust other than water.

To Joseph Pratt, that sounds like an ideal way to run a boat.

Pratt is co-founder of an Alameda startup developing a prototype ferry powered by fuel cells, the same technology inside the Honda Clarity sedan and the Toyota Mirai.

It will be, Pratt says, the first such boat in the United States. And if it works as planned, it could give the global maritime industry a way to tackle air pollution and global warming emissions in one step.

Pratt studied fuel cells for years as an engineer at Sandia National Laboratories and, in 2017, co-authored a study looking at how well the technology might work in a range of vessels, from giant container ships to fishing trawlers and passenger boats. As far as he could tell, fuel cells could power them all.

“I did this study in part to see what was the limit to using hydrogen fuel cells, and the most surprising thing to me was I didn’t find one,” he said.

Now his startup, Golden Gate Zero Emission Marine, is part of a team that has received a $3 million state grant to build the fuel-cell ferry, dubbed “Water-Go-Round.”

The boat should hit the waters of San Francisco Bay in autumn 2019. Red and White Fleet will operate it, while Sandia studies its performance. (Two Red and White Fleet executives — Thomas Escher and Joe Burgard — co-founded Golden Gate with Pratt.)

Sandia will forward its findings to the California Air Resources Board, which will use the information to gauge how well fuel cells function in boats. The board, which runs most of California’s global warming programs, provided the grant, using money from the state’s cap-and-trade program for cutting greenhouse gas emissions. The Bay Area Air Quality Management District will administer the project.

California has thrown great effort into promoting electric cars as a way to fight global warming. But that technology is an ill fit for most marine vessels, other than those doing very short trips close to shore.

Current batteries, for example, can’t begin to power a container ship hauling cargo from Hong Kong to Oakland. A 2014 study from the International Maritime Organization estimated that shipping accounted for 2.8 percent of global greenhouse gas emissions from 2007-2012.

“When you’re on the bay, you can’t really plug those engines in,” said Bonnie Soriano, chief of the board’s freight activities branch. “So it’s a challenging sector to get to zero emissions.”

The board also has a long-running interest in cleaning up the air around ports, which tend to be located near lower-income communities. If fuel cells can indeed be made for various vessel types and sizes, they could provide a solution.

Much like battery-powered cars, fuel-cell vehicles use electric motors. But they get their electricity from a fuel cell, which uses an electrochemical reaction between hydrogen and oxygen to generate current. The only by-products are heat and water vapor. The hydrogen is stored on-board, in specially designed tanks.

The Water-Go-Round, as designed, will store enough hydrogen to run for up to two days between refueling. The 70-foot-long aluminum catamaran will boast a top speed of 22 knots (about 25 mph) and have room for 84 passengers. Bay Ship & Yacht Co. of Alameda will build it, using dual electric motors from BAE Systems and a set of fuel cells from Hydrogenics. It will refuel from hydrogen-carrying trucks, not requiring any special dock-side infrastructure.

Pratt’s company, founded last year, won’t become a shipbuilder, he said. Instead, it plans to develop and sell the drivetrain technology that can be added to new or existing boats.

“Engines don’t last as long as boats, so we’ve got an opportunity to help owners replace those engines with something cleaner,” Pratt said.

David R. Baker is a San Francisco Chronicle staff writer. Email: dbaker@sfchronicle.com Twitter: @DavidBakerSF