Cruising Guide to the San Juan Islands: Top Anchorages, Marinas, Public Docks, and Activities

Planning a boating trip to the San Juan Islands? This post offers highlights from my larger in depth cruising guide—both here on the website and in print—with some of my favorite anchorages, marinas, public docks, and onshore activities for boaters visiting the islands.

Whether you're sailing a trailerable sloop, motoring a pocket trawler, paddling a kayak, or even pedaling a bicycle, this is a good time and place to start planning your next island cruise.

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Best Anchorages in the San Juan Islands

The islands are full of protected coves that make excellent overnight anchorages. These are just a few personal favorites—places I return to often and recommend to friends:

• Echo Bay, Sucia Island – Popular but spacious. Good holding, solid protection, and miles of trails. Don’t miss the China Caves sandstone formations ashore.
• Reid and Prevost Harbors, Stuart Island – Two peaceful harbors on one island. Mooring buoys, dock space, and a rewarding hike to Turn Point Lighthouse and museum.
• Garrison Bay, San Juan Island – Sheltered, calm, and full of history. Visit English Camp National Park, where a pig once sparked a 12-year standoff between Britain and the U.S., and then hike up picturesque Young Hill for a memorable view of your boat far beloe.
• Hunter Bay, Lopez Island – A quieter anchorage with a small public dock and easy access to the relaxed pace at the southern end of  Lopez Island. (perfect for cruising bicyclists)

Each anchorage has its own rhythm. Some offer quiet solitude, others put you close to nature, tidepools, trailheads, or even a warm cinnamon roll on shore.

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Marinas and Public Docks for Cruisers

When you need shore power, fuel, supplies—or just want to tie up and stretch your legs—there are plenty of marina and public dock options across the San Juans:

• Friday Harbor Marina – The busiest harbor in the islands. Fuel, groceries, restaurants, ferry service, and access to a lively town.
• Roche Harbor Resort – A full-service marina with a resort feel. Watch the sunset flag ceremony (complete with cannon fire), grab a meal, and browse the sculpture garden.
• Deer Harbor Marina (Orcas Island) – Small, friendly, and a good base for kayaking or a short walk.
• Blakely Island Marina – Quiet and convenient, with fuel and a small store right at the dock.
• Public Use Docks – Nearly every major island has a county, state, or DNR dock open to the public. Great for short stops, gear loading, or access to island hikes and roadways.

These aren’t the only options—just a few that stand out. This website has more detailed pages on public use docks, marinas, and smaller spots that many boaters overlook.

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Visiting the Islands: Things to Do Ashore

Cruising the San Juans is as much about what happens off the boat as on it. Every island has its own pace and personality, and there’s no shortage of ways to explore:

• Hiking – Mount Constitution and Turtleback Mountain (Orcas Island), Young Hill (San Juan Island), and the lesser-known Eagle Cliff trail on Cypress Island all offer incredible views.
• Wildlife Watching – Orcas, porpoises, bald eagles, and seals are common sights. Lime Kiln Point on San Juan Island is one of the best land-based whale-watching spots in the world.
• Towns and Villages – Friday Harbor, Lopez Village, and Eastsound are worth stepping into, each with its own galleries, bakeries, and market days.
• Local History – Walk through American and English Camps, visit the San Juan Island Historical Museum, or explore the quirky Roche Harbor Mausoleum.
• Quiet Moments – Paddleboard a glassy inlet, read on a driftwood beach, or relax by a fire in one of more than 20 waterfront campgrounds.

Whether you're visiting for a weekend or several weeks, you’ll find plenty of reasons to linger ashore.

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Cruising Tips and Seasonal Notes

A few practical thoughts from years of island cruising:

• Best Time to Visit – July and August offer the best weather, longer days and beautiful flowers, but spring and fall bring quieter anchorages. Late May and September are favorites of many longtime cruisers, but some parks and businesses may be closed.
• Tides and Currents – Don’t let the charts or icky reviews scare you. With smart planning, even tricky spots like Deception Pass, Obstruction Pass, and Cattle Pass are easily and safely transited. I’ve shared tips elsewhere on this site to help take the stress out of it.
• Mooring Balls – Available throughout the San Juans and Washington State Parks, county docks, and DNR-managed marine areas. As with docks, they’re all first come, first served—so bring your anchor and rode, and you will never go away unhappy.

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Final Thoughts

This post is just a taste of what the San Juan Islands have to offer. My goal is to help you discover your own favorite spots—whether that’s a peaceful anchorage, a well-placed dock, a friendly marina, or a shore activity that makes the trip unforgettable.

This website is part of a larger project to share practical advice, lesser-known locations, and the kind of local cruising knowledge you only get by doing. If you're looking for more detail, check out the full printed cruising guide, and other posts here on the site. They go deeper into routes, itineraries, harbors, and planning—and the printed cruise guide book fits nicely in a nav table, dry bag and makes a great present.

If you’re planning your first trip or your tenth season, keep exploring. The San Juans always have more to offer.