4 Ways to Cruise the San Juan Islands

October 27, 2023 • Lis Larson
Our experts detail their top San Juan Islands cruises. Travel close to home in this magical archipelago ripe with birds, marine wildlife, regional delicacies and tasting rooms.

With 408 miles of shoreline and 172 named islands, Washington’s San Juan Islands are best explored by small ship. Below we detail a selection of San Juan Island cruises that allow you to access this close-to-home archipelago in style and ease.

Expect to meet pods of orcas feasting on salmon, playful seals and sea lions lounging on rocky islets, black bear and deer flourishing in deep evergreen forests, as well as royalty atop the trees since the region hosts the highest concentration of bald eagles in the Lower 48. The San Juans are also dubbed the “Gourmet Archipelago” with culinary festivals, shellfish farms, vineyards, breweries, distilleries and tasting rooms. Let’s go!

IN THIS POST – 4 Ways to Cruise the San Juan Islands:
1. Cruise on a Historic Small Yacht – 6 days, round-trip Bellingham
2. Take a National Geographic Cruise – 8 days, round-trip Seattle
3. Pass by en route to Alaska – 13 days, Seattle to Juneau
4. Book a Private Boat Charter

On a San Juan Islands cruise two guests stand onboard with a camera facing the sun setting over an island in the distance.
Photo by David Vargas

1) Cruise the San Juans on a Historic Yacht

The 6-day Voyage Through the San Juan Islands aboard 12-guest Catalyst offers cruises round-trip from Bellingham, Washington—a short drive, flight or shuttle bus ride from Seattle. Experience the emerald jewels of the San Juan Archipelago on this close-to-home voyage, with daily opportunities to experience nature in an active way while also tasting local foods, beer, wine and spirits. Start each morning with a walk or kayak paddle and spend each afternoon visiting with the vintners, brewers and distillers that the Pacific Northwest is known for.

Westward exterior picture of starboard side with pine trees in background.

The Catalyst is an intimate small ship offering historic charm and hearty, experienced crew members with character. The crew will surely be among the highlights of your Puget Sound and San Juan Islands cruise. Her original 1932 Washington Diesel engine is the only one like it in the world, so history and boat aficionados will love sailing the San Juans on this boat. Plus there’s the ship’s gourmet cuisine paired with the beers, wines and spirits discovered daily on her Puget Sound cruises.

2) Take a National Geographic San Juan Island Cruise

The newest ship to offer San Juan cruises, via the 8-day Exploring British Columbia & the San Juan Islands trip, is the 100-guest National Geographic Venture. This purpose-built expedition vessel launched in 2018, in California, and now embarks on regularly scheduled departures. Get on this ship for the excellent expedition staff, high-tech exploration and educational equipment.

National Geographic Venture is state-of-the-art, a vessel made for exploring coastal waters, shallow coves and fast-moving channels thanks to her shallow draft that draws only nine feet of water. This allows her to sail into places where much larger ships cannot go, and further setting her apart from other San Juan Island cruise ships is a guide complement that includes a historian, a geologist/naturalist, a wellness specialist and a Lindblad-National Geographic certified photo instructor.

Exterior shot of National Geographic Venture ship in the open sea.

Her San Juan Island cruises operate round-trip from Seattle. Two days are spent cruising Puget Sound and the San Juan Islands by expedition landing craft, kayak, paddleboard and hike, with a special stop at picturesque Friday Harbor to visit the Whale Museum and local shops. The world-class Canadian city of Vancouver is a nearby option for bonus travel before or after exploring the San Juan Islands by boat,.

3) Sail Past the San Juans in Route to Alaska

If you want to see the best of the Northwest and don’t mind just passing through the San Juans more quickly, a good choice is the comprehensive 13-day Inside Passage with Olympic National Park & 2 Days in Glacier Bay aboard the 22-guest Safari Quest, 36-guest Safari Explorer, 84-guest Safari Endeavour or 86-guest Wilderness Legacy. This trip visits two UNESCO World Heritage Sites—Glacier Bay National Park and Olympic National Park—plus offers opportunities for kayaking, stand-up paddleboarding, hiking, beach combing and enjoying guided skiff rides. 

A stand-up paddle boarder floats in front of the Safari Quest on Alaska's Inside Passage & San Juans Cruise.

There’s no dedicated day in the San Juan Islands, but you will sail past them. Add to this stops in Canada’s Inside Passage and Alaska’s Misty Fjords National Monument, Ketchikan and Glacier Bay National Park, and you truly have a trip that goes beyond what any other San Juan cruises do.

4) Book a Boat Charter San Juan Islands

A yacht charter in the San Juan Islands is an ideal vacation if you want to choose your own route and activities. You can actually save money when you book a San Juan Islands boat charter as blocking out a whole ship for your group costs less per cabin than booking on regularly scheduled San Juan cruises. Our most popular yachts to charter in the San Juan Islands are the 12-guest Catalyst and the 22-guest Safari Quest, but the larger expedition ships listed above as well as other yachts may be available for charter cruises.

Note that charters are limited by the ships’ locations as these yachts also position up for small ship Alaska cruises. Your best bet to secure a private charter in the San Juan Islands is to travel in the seasons that these ships are positioned around Seattle: spring and fall. Contact our experts to discuss your charter options for San Juan Island cruises. We can ensure you know what San Juan cruises and Puget Sound cruises are available for your group.

A woman in an AdventureSmith Explorations tan hat smiles standing in front of the waterfalls of Krka National Park in Croatia


You’ve got questions.
We’ve got answers.

This post detailing San Juan Island cruises is among AdventureSmith Explorations’ extensive collection of Small Ship Cruise Guides. Learn more about Pacific Northwest cruises or contact us any time for a personalized recommendation on San Juan Island cruises from Seattle, Vancouver and Alaska; cruising Puget Sound; and yacht charter options in the San Juan Islands. Feel free to ask us your questions about San Juan cruises right in the comments.

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  • Dorene Wackerfuss says:

    We are going to celebrate our 50th anniversary. We did a small ship cruise in Alaska 20 years ago but never in this area. Our adult children would make it 6 of us. Is there a charter we could do for around 5 days in August? There are teachers in the group who would not be able to go in September.

    • AdventureSmith Explorations says:

      Hi Dorene,
      What a wonderful way to celebrate your milestone! If you enjoyed Alaska, you will love the San Juan Islands. An Adventure Specialist will be in touch soon to help you hone in on the ideal ship with August availability.

  • Leonard Allan Russ says:

    We will be celebrating our 20th wedding anniversary 10/4/23 and have a great love for the San Juans and the NW in general. Would you suggest a 3-day tour (possibly longer) for the two of us seniors who will be 79 and 81 at the time of the trip. We are in reasonably good shape, healthy, and love anything outdoors and on the water. One of us is limited in range of walking but short jaunts are fine. We still run our small boat and enjoy some biking (one a recumbent) but cannot imagine anything better than a few days in the San Juans. Suggestions are welcome as we probably need to plan early.

    • AdventureSmith Explorations says:

      Thanks for your question Leonard, and congratulations! Small ship is the best way to explore the many islands of Washington’s San Juan’s plus, an even more incredible way to celebrate such a milestone. While you will find single day and shorter 3 day cruises out of Bellingham, we are strong proponents that longer is better. There is so much to see and do, we focus on longer itineraries ranging from 6 to 8 days – the shortest being the 6-day Voyage Through the San Juan Islands aboard historic yacht 12-guest Catalyst. If you would like to talk about this itinerary please don’t hesitate to contact our experts.

  • Betsy miller says:

    Would like an itinerary to see the San Juan’s by a personal yacht

  • Brandi says:

    I am interesting in an an-inclusive charter, with captain/staff, in late August or September 2021. For perhaps 6-8 ppl. Is this something you do? For a week or so…

    • AdventureSmith Explorations says:

      Hi Brandi, thanks for your comment.
      Yes, our charter cruises are both all-inclusive and fully crewed charters. Having an expert team aboard is essential to a safe and successful voyage. An Adventure Specialist will be in contact with you soon to help you find the right charter ship and the trip for your group.

  • Janis says:

    Thinking about an all inclusive trip thru the San Juan worn family to celebrate our 50th wedding anniversary. There would be 10-15 people. Interested in only our family on the boat.
    Would that be the 8 day, 22 passenger trip?
    If so 9-8 days is too long for most.

    • AdventureSmith Explorations says:

      Hello Janis,
      What a great way to celebrate an anniversary! Congratulations! Chartering a boat with this size group is a great idea and often offers more flexibility for creating unique itineraries. An Adventure Specialist will be touch to help you sort your options.

  • Janet Alford says:

    We are late trying to find something, but interested in a trip through the San Juan Islands from Seattle. Three, four or five days…a nice boat. Nothing too big. Anything available in mid to late June or are we too late? Two of us, two beds.

    • AdventureSmith Explorations says:

      Hello Janet,
      Our shortest San Juan Islands small ship cruise from Seattle is the 8-day Exploring British Columbia & the San Juan Islands aboard the National Geographic Venture, which cruises the San Juan Islands then extends north through the Strait of Georgia. This 8-day schedule offers many more opportunities to see orca whales, eagles and other wildlife that might not be as plentiful on a shorter cruise. If you are able to spend a few more days in the Pacific Northwest, this round-trip Seattle cruise is truly an experience of a lifetime. One of our Adventure Specialists will contact you to discuss your options and to help guide you through the decision making process.

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