John Sayles read Frank Ray Perilli's script for the film once and then totally scrapped it. Sayles said it was set in Milwaukee and explained that the alligator grew gigantic because of beer from a beer factory going into the sewers.
As in the shooting of this film's main inspiration, Jaws (1975), the mechanical, giant alligator was often malfunctioning. In a few scenes, Lewis Teague either shot around the alligator to build suspense or shot a regular alligator in miniature sets (which is plainly obvious in some shots).
According to director Lewis Teague the film was supposed to be scored by James Horner who actually wrote a full score. However due to some sort of a strike he could not record his score so he was replaced by another composer.
The trivia items below may give away important plot points.
In the scene in the sewers where young officer Kelly sneaks up on Forster as a prank, the two take a look at the map and just at that moment, one of their flashlights shines on the area behind them for barely a second showing the audience that the alligator is standing on a platform behind them.
It is heavily implied that the little girl from the beginning of the movie is herpetologist and Forster's love interest Marisa as a child. It is also heavily implied that her pet baby alligator, whom she named Ramon, is the giant man-eating alligator as a youngling. In an ironic example of a Butterfly Effect Theory, if her dad had let her keep the alligator, she and Forster's character would probably never have met.