Filming of the show took place at the CBS Radford Studios complex in Studio City, California. The same stage was later used by The Mary Tyler Moore Show and Roseanne (which featured Gilligan's Island prominently on one episode). The lagoon was drained and used as a parking lot during the show's off-season and was the last surviving element of the show when it was demolished in 1997 as part of an expansion project.
Cave scenes were shot in Newport Beach, California, across from the southern tip of the Balboa Peninsula, in a park just off Ocean Boulevard. The rock jetties at the entrance of Newport Bay can be seen during the opening theme during the line "A 3-Hour Tour" as the Minnow heads out to sea.
Four different boats played the part of the S.S. Minnow. One was used in the opening credits and rented in Ala Wai Yacht Harbor in Honolulu, Hawaii. Another boat, the Bluejacket, was used in the opening credits shown during the second and third seasons and eventually turned up for sale on Vancouver Island in August 2006, after running aground on a reef in the Hecate Strait on the way south from Alaska. One boat was used for beach scenes after being towed to Kauai in Hawaii. The fourth Minnow was built on the CBS Studios set in the second season. The Minnow got its name in an ironic joke. It was named for Newton Minow, chairman of the U.S. FCC, who was most famous for describing television as "a vast wasteland".