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Filming on water came with a lot of unforeseen problems. Scenes taking place inside the 2,204,622.62 pound floating atoll set could be filmed just off the coast, but for scenes taking place on open water, it took hours to bring the set and ships at least two miles off the coast to get a view that offered 270 degrees of open water. Turning the set or the trimaran so that the camera wouldn't pick up land was also very time-consuming. There was limited space on the sets for cameras and their operators to move, and they also had to compensate for the motion of the sea. Local weather conditions usually deteriorated in the afternoon, so most filming had to be stopped after 3 or 4 PM. To make matters worse, about 30 additional boats used by the cast and crew were needed for lighting, cameras, make up, catering, costumes etc., none of which had bathrooms. Filming had to stop repeatedly so people could be ferried to portable toilets on a barge anchored near the shore. All these limitations usually allowed for only five or six setups on each day of filming, significantly extending the shooting schedule.
The preferred three-hour cut of director Kevin Reynolds was drastically edited back to a 135-minute theatrical version by Kevin Costner and the studio, probably in an effort to recoup the film's inflated $175 million dollar budget (since Costner's previous 3-hour movie Wyatt Earp (1994) had been a box office bomb). ABC later broadcast an extended TV version that restored almost 40 minutes of deleted scenes, which explain more about the world, the people who live there, the Smokers' religious beliefs and their ability to refine crude oil. The additional scenes also tie up several loose ends in the theatrical release. Being a TV special, this version was also censored for violence and language. A fan-edit of the film, called 'Waterworld: The Ulysses Cut' (named after a restored scene at the end), was later made in an attempt to create the most complete version of the movie. It was compiled from several broadcast versions, containing all of the additional footage from the TV version while restoring the previously censored parts. In an unexpected turn, the original distributor officially sanctioned this fan-edit by releasing it in a box-set with the other two versions. This Ulysses Cut was remastered in high-definition though, created with original footage rather than lower-quality broadcast material.
It is rumored that director Kevin Reynolds and Kevin Costner had a huge squabble over the film, resulting in Reynolds walking off the project, and leaving Costner to take over directing and oversee editing. Reynolds was quoted as saying that "Kevin Costner should only star in movies he directs. That way, he can work with his favorite actor and favorite director."
For the Japanese premiere, Kevin Costner had his private plane flown to Tokyo. He failed to get permission to store his plane at the airport for the duration of his trip. He asked the Navy if he could use their airport at Atsugi. They agreed, but only if Costner showed the movie there, and made a personal appearance.