The helicopter, a Robinson R-22, experienced engine problems and landed near Embarcadero Road and Highway 101 in Palo Alto, spokesman Ian Gregor said.
The pilot was the only person on board and did not appear to be injured, Gregor said.
The aircraft is registered to Parker Helicopter, LLC in Capitola in Santa Cruz County.
The helicopter landed on its side in about 4 feet of water.
Emergency crews responded to the scene and the FAA and the National Transportation Safety Board are investigating.
ABC7 contributed to this report