Stores in spring at Roche Harbor. San Juan Islands are located in the heart of the Salish Sea, north of Seattle, Washington, east of Victoria, British Columbia, Canada, and south of Vancouver, British Columbia, Canada. There are 172 named islands and reefs in San Juan County. The three largest and most populous are San Juan Island, Orcas Island, and Lopez Island. The islands can be reached only by ferry or float plane. There are no bridges between the islands.