Troung, 30, was boating with his father when their dinghy was hit by a motorboat around 12:25 p.m. Wednesday.
The impact caused the dinghy to flip over, sending the pair into the water, according to the U.S. Coast Guard.
The father was able to climb on top of the capsized hull of the vessel but Troung was trapped underneath, Coast Guard officials said.
Both men were eventually rescued and taken to San Francisco General Hospital, where Truong was pronounced dead.
The father was in stable condition as of Wednesday night, according to the Coast Guard.
Brisbane police are investigating the collision. Sgt. T. Lynn said police interviewed people from both boats on Wednesday.
Anyone with information about the accident is asked to call Brisbane police at (415) 467-1212.