The movie was primarily shot at Three Caves, an abandoned quarry, in Huntsville, Alabama. Also in North Alabama, is Cathedral Caverns, where the 1984 Timothy Bottoms movie "What Waits Below" was filmed. Bill Schweikert was a grip on "What Waits Below" and was back as cinematographer for "Moles".
The original/working title of the film ("Like Moles, Like Rats") comes from a line in the Thornton Wilder play, The Skin of Our Teeth.