Santa Cruz police say officers were called to an area near the mouth of the river by witnesses who saw the man's body around 8:30 a.m. Saturday.
There were no signs of foul play and the cause of death has not been determined. It was not known how long the body was in the river.
After the man's body was recovered, investigators canvassed the area and interviewed the witnesses who called police.
The San Lorenzo River originates in the Santa Cruz Mountains and flows nearly 30 miles before emptying into Monterey Bay.