It's a five day trial, but transportation officials say based on how smoothly the service runs, it could become permanent.
Google will pay the Transportation Authority $275 per landing.
The company is also providing off-site parking in Alameda and a shuttle service for its employees, in order to not disrupt regular commuters.
Google employees declined to comment, but many regular ferry commuters say they're in favor of the move.
"I think it takes less congestion off the freeways. The waterways aren't used enough. You know, we used to use them more. I think it's fabulous. As long as they don't mess up with our parking," ferry commuter Sue Trigg said.
Last month, Google started a similar trial ferrying its employees between San Francisco and Redwood City.
Both trials end this Friday.
Protesters have rallied against Google and other tech companies using shuttle buses which have become a growing symbol of economic inequality in San Francisco.
Cornell Barnard contributed to this story.