Crews from the Coast Guard were dispatched to the area around 12:30 p.m. after learning that the dinghy had overturned and the two people on board had been thrown into the water.
One of the victims was able to cling to the side of the boat until rescue crews arrived and a second person was pulled from the water. Rescue divers re-entered the water just before 3 p.m. to search for a possible third victim, but the search was cancelled once it was conformed there were only two people aboard the boat.
San Francisco resident Luis Avalos saw both men being treated.
"That guy, you know, they were doing CPR, trying to gte him back alive and stuff, then a few minutes later, another boat came in and they got, they had another person, but he was alive and stuff, he was moving around, he looked banged up, some kind of accident, I don't know," Avalos said.
Both men, believed to be a father and son, were transported to the hospital. The son, Minh Truong, later succumbed to his injuries. The father is reported to be in good condition.
The cause of the collision has not been determined.
Stay with ABC7NEWS.COM for updates on this developing story.