The standard way to reach Friday Harbor is by Washington State Ferries from Anacortes, on the mainland east of the islands. The ferry ride takes about an hour and a quarter to Friday Harbor, passing through the archipelago with views of forested islands and, in summer, frequently marine mammals. In summer, reservations for vehicles are essential — walk-on passengers can usually board without booking, but vehicles queue for hours without a reservation.
Kenmore Air and Harbour Air operate floatplane service from Seattle, landing directly in Friday Harbor harbour. The flight takes about 35 minutes and is far more expensive than the ferry, but the aerial view of the islands is spectacular and the convenience significant. San Juan Airlines flies small aircraft from Anacortes and Bellingham.
From Vancouver, Canada, BC Ferries connects Sidney (near Victoria) to San Juan Island through the inter-island ferry system, though US Customs formalities apply on arrival. Passenger-only fast ferries from Bellingham run seasonally. If you are arriving without a car, the town is walkable and the island has a limited bus service in summer, supplemented by taxis and bicycles for hire.