Fire personnel responded to Petaluma Boulevard South and Mountain View Avenue after receiving a call about the capsizing at 12:36 p.m.
A man in his mid 60s had capsized his kayak in the mud on the east shore of the river, and people nearby had used an aluminum boat to pull him from the mud, according to the fire department.
Fire units arrived at the scene at 12:40 to find the man in the boat at the dock's edge. Personnel provided basic life support before transporting the victim by ambulance to a nearby hospital.
The victim's name and condition are being withheld.