The incident, which was caught on tape, happened shortly before three o'clock near the Clark Street Bridge.
Police say the kayaker didn't see what happened but people on shore alerted him to the man in the water. The kayaker then stepped in to help until the police marine unit arrived.
"The kayaker was a Good Samaritan citizen that was on scene and that held this man's head out of the water until we were able to get there and get him on board our vessel," said Officer Mark Jaeger, Chicago Police Department.
The man who fell into the water was taken to Northwestern Memorial Hospital in critical condition. Police say he is from Chicago.