For most people, bicycling the San Juan's means arriving with your bike and gear in a car on a Ferry.
But it doesn't have to be this way. Savvy cyclists leave their cars in Anacortes and ride the ferry to the San Juan Islands. Once in the islands bicycle travel is the way to go.
First let's explore a likely scenario for those without a boat, bear with me, this will get a little wordy:
You drive to Anacortes and find a place to park for free for a week, maybe more. Or park at the ferry terminal long term parking lot for about $40 per week. Next, jump on the ferry paying a small nominal fee for one passenger and bicycle for a lift to Friday Harbor on San Juan Island, or Orcas, or Lopez, or Shaw. FYI: foot passengers and bicyclists never need reservations or need to wait in line like car travelers.
So far so good!
The day is still early, start touring (ride your bike). At the end of the day you will end up in a motel, B&B, campground, or any number of resorts. You probably will be well advised to have some reservations lined up in advance. Oh, and bring a pocket full of cash because restaurants and beds aren't free. The next day tour around some more then jump on the free for foot passengers Ferry to other Islands and repeat. Eventually you will end up back in Anacortes where your car is waiting for the drive home.
This is a great plan if you are into minimalist and don't have a boat, but there are a few weaknesses; number one, where is all my extra gear that I take when I travel, oh yeah its back in the car parked in Anacortes while I'm gallivanting around on an island with nothing but my pocket full of cash and what fits in my bike bags. (not good for some of us) Excellent plan if your a hard core bicyclist. Number two doesn't matter, I'm still back on number one.
Ok, here's the boating/bicycling scenario: