Bay Minette, AL. Point Clear, AL. and Mobile, AL were used for filming locations. They actually had a crocodile wrangler with a gun on set, "just in case".
The houses for the film were built specifically for the movie in Alabama, and were just shells of houses. It was done this way mainly because of the ending of the film. The lake is Byrnes Lake.
The interiors of the house were also built for the film. Some were filmed in a warehouse in LA, while others were filmed in Topanga Canyon, California at the house Friday The 13th Part 4 was filmed at.
One scene said to be filmed at the Friday 4 house, is the scene where Jason is standing outside the window looking in and Robin's death scene which had been reshot.
Some of the water scenes were filmed in Malibu Canyon Creek in Mobile, AL. And a Scuba school tank was used for underwater scenes.
The tool shed was actually built in the studio.