In the pilot and the newer footage in the Christmas ep with the regular cast and least two other eps (the glue ep and the Skipper+Gilligan raft ep) the Castaways are shown on a real beach. Later on we only see them at the in real-life man-made lagoon. In the ep where Ginger had the crystal ball Skipper and Gilligan are supposed to be down at a beach again but it's obvious the actors weren't really on the real thing this time.