According to the sleeve notes on the DVD, a dry for wet lighting test by Alex Thomson used an old army tank for the wreck of the Leviathan,and some make shift diving suits were made using padded football suits and helmets from 2010: The Year We Make Contact (1984).The final suits in the film were designed by Steve Burg and built by Stan Winston's crew.
In designing the creature of the film, Stan Winston and George P. Cosmatos went through a mini-library of marine life pictures and medical reference books. They were inspired by the physiology of the natural world, and came up with the idea of combining human body parts and elements of deep sea marine life into an unnatural creature never seen on film before.
There are very few scenes in the film that were actually shot underwater, as production went for the "dry for wet" look. With most of the scenes inside the Shack taking place on soundstages and a tank measuring 130ft x 270ft.
While much has been written about Doc's (Richard Crenna) Latin quote, a fast and loose translation of, "Natura non confundenda est" is "Nature is not to be confused".
Chicken feathers were used at one point of shooting the underwater sequences to suggest things were floating around in the water. According to Alex Thomson this did not work because the feathers floating side to side instead of up and down and the idea had to be scrapped altogether.
Hector Elizondo's character of Cobb is named after the film's production designer, Ron Cobb. Also, Michael Carmine's character of Tony 'DeJesus' Rodero, shares the same last name of the film's first assistant director, 'Kuki Lopez Rodero'.
Not only does this film have a similar theme (deep ocean scientific studies) to DeepStar Six (1989) which was released the same year, but the plots are also almost identical: The science team comes across an unknown organism in extreme depth, it hunts them one by one, and finally follows the few survivors up to the surface.