Firefighters received word at 9:52 a.m. that the boat was sinking.
San Jose fire Capt. Mary Gutierrez said there were two people aboard the 28-foot boat when it ran into problems this morning.
"They were out shrimping for the day and they noticed about 4 miles out that the boat was taking on water, so they headed in to the marina," Gutierrez said.
On the way in, they tried to bail the water out of the boat by hand and managed to make it back to the marina, she said.
The captain called 911, and when the boat arrived, firefighters helped pump water out of the vessel to try to keep it from sinking.
"Before we could, the boat sank," Gutierrez said.
Shortly before 1 p.m. it was almost completely submerged, she said.
Gutierrez said about 150 pounds of shrimp went down with the boat, which was carrying an estimated 30 gallons of diesel fuel.
She said it does not appear any fuel has spilled but that the California Department of Fish and Game and the Coast Guard have been notified of the incident.
Absorbent boom is being prepared in the event that a spill occurs.
The captain suffered a cut to his head while he was bailing out water from the boat and was treated at the marina, she said. Other than that, the boaters were OK.
"They feel very fortunate to have been able to make it back that four-mile journey to the marina here," Gutierrez said.
