This close-to-home archipelago is our top pick for autumn travel this year as its 408 miles of shoreline are easy to access and are a foodie and wildlife lover’s hotspot. How will you choose to small ship cruise the San Juan Islands?

A view from a vista point of a Pacific Northwest body of water with green mountains jetting into the water, seen from a cruise to the San Juan Islands.

This close-to-home archipelago is our top pick for autumn cruising as its 408 miles of shoreline are easy to access and are a foodie and wildlife lover’s hotspot.

The San Juan Islands are located just off Washington State’s coast north of Seattle and east of Victoria, British Columbia. Sailing among the 172 named islands of the San Juans, 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, as 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, four shellfish farms, three vineyards, one brewery, one cidery/distillery and seven tasting rooms featuring local and regional wines, micro beers and locally distilled spirits.

Below we detail four San Juan Island cruises available aboard a variety of small expedition ships. Read on, or simply contact us; our Adventure Specialists are standing by to give you a personalized travel recommendation.

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) Voyage Aboard a Historic Yacht on Friday Harbor Cruises

The 6-day Voyage Through the San Juan Islands aboard 8-guest Westward offers cruises from picturesque Friday Harbor in 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.

Island hop aboard the Westward, a purpose-built adventure yacht registered as a Historic Place by the National Park Service. This intimate small ship offers historic charm and hearty, experienced crew members with character, plus gourmet cuisine paired with the beers, wines and spirits discovered daily on her Bellingham cruise.

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

2) Cruise Aboard the Newest San Juan Islands Ship: 100-Guest National Geographic Venture

The newest ship to sail the San Juans, via our 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 next fall for an 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 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.

Departures are from Vancouver, BC and Seattle. Two days are spent exploring 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 their wilderness cruise.

3) Sail on the Luxury 22-Guest Safari Quest

The 8-day Olympic Wilderness & San Juan Islands aboard the intimate, luxury 22-guest Safari Quest offers the most time and flexibility exploring the San Juan Islands. You’ll spend at least three 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!

4) Sail the Alaskan And Canadian Inside Passage Aboard Active Small Ships

The comprehensive 13-day Alaska’s Inside Passage & Glacier Bay Wilderness Cruise aboard the 36-guest Safari Explorer, 74-guest Wilderness Explorer, 76-guest Wilderness Discoverer or 84-guest Safari Endeavour 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 for a full day amongst the San Juan Islands. Add to this stops in the quiet reaches of Puget Sound’s Hood Canal, Canada’s Great Bear Rainforest, Misty Fjords National Monument and Ketchikan, Alaska.

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

Learn more about Pacific Northwest small ship cruises or contact AdventureSmith’s experts any time for other travel ideas for the autumn season.

This post detailing San Juan Island cruises is among AdventureSmith Explorations’ extensive collection of Small Ship Cruise Guides. While originally published in 2017, our team of experts have since updated the content to reflect any changes; our most recent update occurred July 2020.