The Coast Guard said it was notified of the crash involving 14 people near Monroe Harbor around 11:45 p.m.
The Chicago Fire Department said five people were hospitalized in serious to grave conditions.
Three people, including a woman in grave condition, were taken to Northwestern Hospital, CFD said. Two others were taken to Stroger Hospital.
Nine other people refused treatment on the scene.
The Coast Guard said both boats involved are considered recreational vehicles.
The Coast Guard towed one boat to Queens Landing across from Buckingham Fountain. Chicago police towed the other boat, which suffered the most damage, to CPD Marine Unit headquarters.
The Illinois Department of Natural Resources is handling the investigation.
What caused the crash was not immediately clear.
Authorities did not immediately provide further information about the crash.
This is a developing story. Check back with ABC7 for updates.