The aircraft crashed into Fogg Dam, Middle Point, at about 10.20am (11.50am AEST).
Fogg Dam is a conservation reserve with waterways inhabited by saltwater crocodiles.
An uninjured 29-year-old woman who was a passenger in the aircraft was airlifted out and taken to Royal Darwin Hospital for assessment.
The 63-year-old male pilot was found dead inside the aircraft.
The investigation is ongoing.
