The crash occurred in the Raccoon Straits near Tiburon at about 4:30 p.m. Saturday.
The ferry was carrying 500 people aboard and was headed from Sausalito to San Francisco when it was struck by the speedboat.
No one on the ferry was hurt but two of the four people aboard the pleasure craft were taken by boat and ambulance to a nearby hospital. No information on their condition has been released.
The ferry reportedly continued its trip to Pier 1 of the Embarcadero after the crash.
According to authorities, the speedboat's speed is suspected to be a factor.