With 408 miles of shoreline and 172 named islands, Washington’s San Juan Islands are best explored by small ship. Below we detail four 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!


1. Cruise on a Historic Small Yacht – 6 days, round-trip Bellingham
2. Take a National Geographic Cruise – 8 days, Seattle to Vancouver
3. Sail on a Luxury Yacht – 8 days, round-trip Seattle
4. Pass by en route to Alaska – 13 days, Seattle to Juneau
5. 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 depart from either Vancouver, BC or 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. We’re thrilled that Vancouver is an embarkation/disembarkation point on this trip, a bonus as travelers can explore this world-class Canadian city before or after exploring the San Juan Islands by boat.

3) Cruise from Seattle to San Juan Islands on a Luxury Yacht

The 8-day San Juan Islands & Olympic Wilderness aboard the intimate, luxury 22-guest Safari Quest offers the most time and flexibility exploring the San Juan Islands. You’ll spend five or more days in this famed archipelago, stopping at Lopez Island, San Juan Island, Orcas Island and Sucia Island, among others. Sail round-trip from Seattle, exploring this city’s waterfront before sailing through the San Juans, dropping anchor for kayaking and hiking. A highlight of this itinerary is Sucia Island’s 564-acre Marine State Park, considered the crown jewel of Washington’s marine park system. This horseshoe-shaped island is accessible only by watercraft and boasts a population of just four residents!

Starting in 2024, these San Juan Island cruises change routes, to the Canadian Coastal & Olympic National Park Cruise. This itinerary still conveniently operates round-trip Seattle but explores farther north, deep into the quiet Canadian coastal mountains. From the comfortable 66-guest Safari Voyager, watch for gray whales, orcas, seals, sea lions, eagles and sea birds, with plenty of birding opportunities. Hike in Olympic National Park. And meet with members of the Makah Nation at Neah Bay.

This trip is also the top choice for travelers seeking San Juan Island cruises from Seattle since it embarks and disembarks in Seattle. This makes pre- and post-cruise arrangements easy. A cruise from Seattle to the San Juan Islands like this saves you from driving two hours from the city or figuring out how to link complicated ferry schedules. Not to mention your accommodations and guided activities are all from the ship for a truly seamless, efficient and hassle free way to travel!

4) 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 & Glacier Bay Wilderness Cruise 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.

5) 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.

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.