Offshore Marine Basin, 578 Enterprise Street, Escondido, California, USA (Whale swimming scenes majority of the final act including Jesse falling from the helicopter and gets rescued by Willy after he nearly drowns. Was Free Willy filmed in the San Juan Islands?ġ1 of 11 found this interesting Interesting?ĩ of 9 found this interesting Interesting? Filming commenced in Astoria, Oregon and the San Juan Islands between April and August 1994 with additional filming taking place in California.Did they use a real whale in Free Willy 2?.