It happened Sunday night on North Friant Road near Copper.
Officials said the three fishermen were heading downstream at sunset. Their boat hit a tree and turned over.
Two of the men were able to swim to shore, the other latched onto a tree.
"It wasn't necessary to put any swimmers in the water at the time because we had a boat in route. We were able to drive right up to the tree, he was able to get in the boat, and we were able to rescue him," said Shawn Erwin with the Fresno County Sheriff's Department.
The men were examined by paramedics on scene and released.
This is the eighth rescue on the San Joaquin River this year.