Washington State Ferries run year round from Anacortes to Orcas, San Juan, Shaw and Lopez Islands. Be sure to make a reservation. You can book your ferry reservation and view up-to-date schedules here. Traveling via car and ferry offers the most flexibility and mobility once on island. Get lucky on a day time ferry ride during summer months, and you may see the Southern Resident Orcas traveling on your route!
By Sea Plane
Kenmore Air offers sea plane flights to the San Juan Islands from Seattle. Connect from Seatac Airport to Lake Union and Boeing Field via their shuttle, included in RT tickets. If you travel via plane, you will likely want to rent a car, as getting around on the island without one is limiting. Taxi service is available on Orcas, though advance reservations are recommended due to their limited availability.