Kona Kai Club opened in 1953, and along with the nearby Bali Hai Restaurant, was one of the first developments on the predominantly Polynesian-themed Shelter Island. The Kona Kai Club was a marina, intended from the start to serve high-end yachts, and it developed into the premiere marina in San Diego. The catalog of celebrities mooring pleasure boats there is impressive: Clark Gable, Burt Lancaster, Jack Lemmon, Gregory Peck, Jimmy Durante, Dick Van Dyke, Liberace, and many more.

The Kon-Tiki bar & lounge adjoined the club's main dining room and came complete with a Kon-Tiki sail waving from the bar itself.

In 1959, the Kona Inn hotel was opened next door (at 1901 Shelter Island Drive). Later in the year, the entire property was purchased by Jack Wrather, a Hollywood producer who was the original owner of the Disneyland Hotel. Wrather expanded the marina, and in 1963 sold the club to John Alessio, owner of the famous Hotel del Coronado. Alessio started to add Mediterranean touches, including an octagonal structure echoing the one at the Coronado.

The Kona Inn and Kona Kai Club underwent their final renovation from 1995-1997, which completed the conversion from Polynesian to Mediterranean. The name was removed in 1998, and it became Shelter Pointe Hotel & Marina.

Today, the name is back (well, nearly: it is called Kona Kai Resort & Spa) but the theming is entirely Mediterranean.