Published by Roam Yacht Charters | November 2024 | 12 min read
After decades of navigating the emerald waters of the San Juan Islands, our captains have discovered something remarkable: the most breathtaking spots aren’t on any tourist map. They’re tucked away in secluded coves, hidden behind rocky outcroppings, and accessible only to those who arrive by water.
While ferry passengers crowd into Friday Harbor and Roche Harbor (both beautiful in their own right), yacht charterers have access to an entirely different San Juan experience. Today, we’re sharing our closely-guarded list of secret anchorages and hidden beaches that make private yacht charters the ultimate way to explore these Pacific Northwest jewels.
Why Some San Juan Treasures Remain Hidden
The San Juan archipelago contains 172 named islands and hundreds more unnamed rocks and reefs. Of these, only four are accessible by ferry. The Washington State Parks system has done an excellent job preserving many marine parks, but countless pristine spots remain known only to local boaters and seasoned captains.
These hidden gems stay secret for good reasons:
- No road access means no crowds
- Challenging navigation keeps casual boaters away
- Limited anchorage space naturally controls visitor numbers
- Local knowledge is required for safe approach
- Tides and currents create access windows
That’s where chartering with experienced local captains becomes invaluable. Our crews know exactly when and how to access these special places safely.
Posey Island: The Pocket Paradise
GPS Coordinates: 48°35’15.0″N 123°02’45.0″W
Best Time to Visit: Early morning for wildlife, late afternoon for photography
Approach Notes: Northwest approach only, watch for kelp beds on south side
Just north of Roche Harbor lies tiny Posey Island – a mere acre of Pacific Northwest perfection. This state marine park is too small for overnight camping, making it an ideal day-trip destination for yacht charterers seeking solitude.
What makes Posey special:
- 360-degree views of Haro Strait
- Frequent orca sightings during summer months
- Easy beach landing for picnics
- Wildflower meadow in spring
- Historic navigation marker from 1800s
Captain’s Tip: Approach from the northwest during slack tide. The south side looks inviting but is riddled with rocks just below the surface. We once watched a yacht learn this lesson the hard way – expensive mistake!
Little Sucia: The Secret Sister
GPS Coordinates: 48°45’30.0″N 122°54’20.0″W
Best Time to Visit: Low tide for beachcombing
Approach Notes: Enter from west side only, minimum 15-foot depth at low tide
While everyone flocks to Sucia Island State Park, its tiny neighbor to the south remains virtually unknown. Little Sucia (locally called “Baby Sucia”) offers everything its famous sibling does, minus the crowds.
Why we love Little Sucia:
- Fossilized shells embedded in sandstone cliffs
- Eagle nesting site on north shore
- Perfect swimming beach on calm days
- Spectacular sunset views toward Orcas Island
- Often have the entire island to ourselves
Wildlife Alert: We’ve spotted river otters here more frequently than anywhere else in the islands. They seem particularly active around the kelp beds on the eastern shore.
Skull Island: The Halloween Hideaway
GPS Coordinates: 48°42’45.0″N 122°59’30.0″W
Best Time to Visit: Afternoon for best light in the caves
Approach Notes: South approach only, watch depth finder carefully
Don’t let the name fool you – this small island near Massacre Bay got its moniker from its shape, not any dark history. What it lacks in size, it makes up for in geological wonder.
Skull Island highlights:
- Sea caves accessible by dinghy at low tide
- Unique rock formations perfect for photography
- Harbor seal pupping grounds (May-July)
- Protected anchorage on south side
- Incredible acoustics in the main cave
Safety Note: Never enter the caves during tide changes. We time our visits for slack low tide, giving guests about 90 minutes to explore safely.
Unnamed Cove, Northwest Orcas Island
GPS Coordinates: 48°41’20.0″N 122°56’10.0″W
Best Time to Visit: Early morning for mirror-calm water
Approach Notes: Narrow entrance, follow GPS precisely
This might be our favorite secret spot. Known only to locals and appearing on no charts by name, this narrow cove on Orcas Island’s wild northwest shore offers perfect protection and stunning beauty.
What makes this cove magical:
- Bald eagle nest directly above anchorage
- Fresh water stream with small waterfall
- Ancient Native American shell midden
- Morning mist creates ethereal atmosphere
- Natural rock seat perfect for meditation
Captain’s Secret: The entrance is only 40 feet wide and requires precise navigation. We’ve brought hundreds of guests here, and they always gasp when we round the point to reveal this hidden sanctuary.
Cemetery Island: Not What You Think
GPS Coordinates: 48°36’15.0″N 123°09’30.0″W
Best Time to Visit: Late afternoon for warm swimming
Approach Notes: Approach from southeast, anchor in 20-30 feet
Despite its morbid name, Cemetery Island is one of the most life-affirming spots in the San Juans. This private island (respect boundaries!) offers a public beach on its south side that few ever visit.
Cemetery Island treasures:
- Warmest swimming water in the islands
- White shell beach unusual for the area
- Resident seal colony on north rocks
- Calm water even in prevailing winds
- Exceptional shelling after winter storms
Local Lore: Named for a 19th-century burial ground, the island is said to be haunted. We’ve never seen ghosts, but the sunset light here can be downright supernatural.
Secret Harbor, Stuart Island
GPS Coordinates: 48°40’30.0″N 123°12’45.0″W
Best Time to Visit: Sunset for golden hour magic
Approach Notes: Western approach at high tide only
Not to be confused with Reid Harbor or Prevost Harbor, this unnamed inlet on Stuart Island’s rugged coast offers solitude impossible to find in the main anchorages.
Why Secret Harbor lives up to its name:
- Invisible from the water until you’re at the entrance
- Rocky barriers create natural hot tub pools
- Resident pair of otters we’ve watched for years
- Wild berry picking in late summer
- Ancient madrone trees frame the shoreline
Tide Warning: This spot is only accessible within two hours of high tide. We once helped tow a boat that got trapped inside at low tide – learn from their mistake!
Wildlife Watching from Hidden Anchorages
One of the greatest advantages of accessing these hidden spots by yacht is the unparalleled wildlife viewing opportunities. Away from boat traffic and human noise, animals exhibit natural behaviors rarely seen from popular viewpoints.
Our secret spots regularly host:
- Orcas: Posey Island and northwest of Stuart Island
- River Otters: Little Sucia and Cemetery Island
- Seals: Pupping at Skull Island, hauled out at Cemetery Island
- Eagles: Nesting at Unnamed Cove and Little Sucia
- Great Blue Herons: Rookery near Secret Harbor
Planning Your Hidden Gems Charter
While we love sharing these special places, we also believe in preserving their pristine nature. Here’s how we help guests explore responsibly:
Leave No Trace: Pack out everything, including organic waste
Wildlife Distances: Maintain 100+ yards from seals, 300+ yards from orcas
Quiet Zones: Engine off or idle in sensitive areas
Timing Matters: Visit during off-peak times when possible
Small Groups: These intimate spots aren’t suitable for large parties
Navigation Challenges and Safety
These hidden destinations require expert navigation. Challenges include:
- Unmarked rocks and reefs
- Strong tidal currents
- Narrow passages
- Variable depths
- Limited cell service
This is why chartering with experienced local captains is essential. Our crews know every rock, current, and safe passage by heart. They also carry emergency equipment and maintain constant radio contact with the Coast Guard.
Best Times to Explore Hidden Spots
Spring (March-May):
- Migrating gray whales
- Wildflower blooms
- Fewer boats
- Variable weather
Summer (June-August):
- Warmest water
- Longest days
- Resident orcas
- Calmest seas
Fall (September-October):
- Spectacular light
- Migrating birds
- Warm water lingers
- Uncrowded anchorages
Winter (November-February):
- Storm watching
- Dramatic skies
- Complete solitude
- Experienced boaters only
Creating Your Custom Hidden Gems Itinerary
Every charter is unique, and we customize routes based on:
- Weather conditions
- Tide tables
- Guest interests
- Wildlife activity
- Physical ability
A typical “Hidden Gems” charter might include:
- Day 1: Depart Seattle, cruise to Posey Island for lunch, afternoon at Little Sucia
- Day 2: Morning at Skull Island caves, afternoon wildlife watching, anchor at Secret Harbor
- Day 3: Explore Unnamed Cove, visit Cemetery Island, return via Deception Pass
Conservation Through Exploration
By sharing these secret spots, we hope to inspire a deeper connection with the San Juan Islands’ wild beauty. When people experience these pristine places firsthand, they become passionate protectors of our marine environment.
Our conservation commitments:
- Educate guests about marine ecology
- Support local conservation organizations
- Report wildlife sightings to researchers
- Maintain strict environmental protocols
- Limit visits to sensitive areas
Your Invitation to Discover
The San Juan Islands hold countless secrets, and we’ve shared just a few. Each season reveals new wonders, and every charter offers unique discoveries. Whether you’re seeking adventure, solitude, or simply the perfect photo opportunity, these hidden gems deliver experiences impossible to find any other way.
The magic of arriving at an unnamed cove, dropping anchor in crystal-clear water, and realizing you have an entire Pacific Northwest paradise to yourself – this is why we do what we do. These moments can’t be bought or scheduled; they must be discovered.
Ready to explore the San Juan Islands’ best-kept secrets? Our experienced captains are standing by to guide you to places most people never know exist. Contact us today to plan your hidden gems adventure.
About the Author: Captain Mike Thompson has navigated the San Juan Islands for over 30 years. When not guiding guests to secret anchorages, he volunteers with the Pacific Northwest Maritime Museum and contributes to regional boating publications.