The pilot, identified as Sharon Yee, 27, co-pilot Fairol Kamil, 33, and student Son Sien Shoong, 22, had taken off from Batu Berendam airport at 7pm on a teaching flight.
The plane belonging to the Malacca Flying Academy encountered engine problem soon after and crashed.
Sharon and Soh managed to swim some 400m to the shore while Fairol, who was trapped in the wreckage, was rescued by firemen at about 9.30pm.
Fire and Rescue Department chief Yazid Mohd Tahir said they were alerted of the incident by people who were praying at a mosque.
The wreckage is expected to be brought to shore tomorrow.