7 Best Snorkeling Sites by Boat on St. John
Want to experience the best snorkeling in St. John? Here are the top snorkel spots you can only reach by boat — perfect for private charters and off-the-beaten-path underwater adventures.
The Best Snorkeling in St. John Isn’t Always Off the Beach
St. John is famous for its incredible snorkeling — but many of the most vibrant reefs, sea caves, and underwater cliffs aren’t accessible from shore. If you want to experience the really good stuff, you’ll need to get on a boat.
Luckily, that’s what we do best.
With over two-thirds of the island protected by Virgin Islands National Park, much of the coastline remains untouched — and that means pristine, uncrowded snorkeling, especially when you venture out by boat. From tiny offshore cays to remote reef walls, these are the snorkel spots that most visitors never reach on their own.
This guide highlights the top snorkel stops around St. John that are only accessible by boat (or best by boat), plus what makes each one worth the trip.
1. Waterlemon Cay — Circle the Cay with Ease (and Skip the Hike)
Yes, you can hike to Waterlemon Cay and snorkel from shore — but the real magic happens when you arrive by boat. Instead of a long hike and surface swim, you can jump right in and easily snorkel the entire perimeter of the cay, including the deeper backside where the reef is healthiest.
This is one of the best places to spot elkhorn coral colonies, schools of tangs and wrasse, and even the occasional reef shark cruising by. The current can pick up around the point, so always check the conditions and snorkel with a buddy.
2. Flanagan Island — Healthy Reefs and Serious Color
Tucked just off the east end of St. John near the BVI border, Flanagan Island is a remote and dramatic snorkel spot only reachable by boat. The reef here drops off quickly, offering crystal-clear water, colorful coral heads, and a chance to see larger marine life like barracuda, rays, and tarpon.
You’ll find healthy coral formations and tons of fish action, especially around the northwestern point of the island. This area is a favorite stop on many full-day charter routes, particularly if the conditions are calm.
Because of the depth and occasional current, Flanagan is best suited for confident swimmers — but it’s one of the most vibrant underwater spots around.
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3. Pelican Rock — Calm Waters and a Local Favorite
While you technically could swim out to Pelican Rock from Hansen Bay, it’s a long haul — and it’s much better (and safer) to visit by boat. Nestled in a quiet pocket off St. John’s East End, Pelican Rock is almost always dead calm, making it ideal for a relaxing, fish-filled snorkel.
You’ll find shallow coral, plenty of reef fish, and often a few surprises like rays or even the occasional turtle. It’s a go-to for local captains looking to sneak in a “secret spot” when the main reefs are busy or windy.
Perfect for beginners and seasoned snorkelers alike — especially if you want something a little off the map.
4. Eagle Shoal — An Underwater Cathedral
Eagle Shoal sits on the southeastern edge of St. John, and it’s as remote and rugged as snorkel spots get. You’ll need a very calm day to make it work, but when conditions line up, this place is unreal.
Expect to see deep coral canyons, reef ledges, eagle rays, nurse sharks, and even an occasional dolphin (although rare) passing through. While there’s a legendary underwater “cathedral” formation best explored by scuba divers, the surrounding reef is still impressive for snorkeling.
This spot is for confident snorkelers only and best visited with a captain who knows the layout — but it’s one of the wildest places you can snorkel in the USVI.
5. Booby Rock — Epic Snorkeling Near Salt Pond
Just offshore from Salt Pond Bay, Booby Rock is a rocky outcrop that juts out of the sea yet remains an under-the-radar snorkel stop around St. John. Only accessible by boat, it’s surrounded by dramatic underwater structure, colorful coral, and big fish cruising through.
You’ll often find schools of jacks and grunts, large parrotfish, and plenty of reef action. Because it’s so exposed, you’ll want to visit on a calm day, but the upside is crystal-clear water and vibrant marine life.
It’s a favorite among captains looking to add a wild-card stop to the itinerary — and a solid pick for intermediate to advanced snorkelers.
6. Tektite — Underwater History Meets Dramatic Terrain
Tucked into a quiet cove on St. John’s remote south side, Tektite is more than just a great snorkel spot — it’s also a piece of underwater history. In the late 1960s, NASA and the Navy built an underwater habitat here for scientific research, giving the site its unique name.
Today, the structures are gone, but what remains is a stunning underwater landscape: dramatic boulders lining the edge of the bay, small caves, ledges, and plenty of hiding spots for fish, octopus, and the occasional nurse shark. It’s all framed by deep, clear water and vibrant coral.
7. Yawzi Point — Quiet Reefs with Big Payoff
Yawzi Point is located between Great and Little Lameshur Bays and offers some of the most underrated snorkeling on St. John. While it’s technically possible to reach it with a long surface swim from shore, it’s far better (and easier) to access by boat, especially given how rough the road is to get there.
This area features healthy reef, unique structures, and a high chance of spotting nurse sharks, squid, angelfish, and even spotted drums tucked into ledges.
Bonus: Because of how hard it is to reach from land, you’ll almost always have this spot to yourself.
🐟 FAQ: Snorkeling by Boat Around St. John
Want a Full St. John Snorkel Guide with Maps, Tips & Local Favorites?
Download our FREE Snorkeling e-book for St. John.
(Get seasonal tips, a marine life guide, and more beach or boat-only accessible sites.)
*After submitting, please check your email for your free guide!*
Most people stick to the shore — but you’re not most people. If you’re dreaming about crystal-clear water, quiet reef ledges, and turtle sightings with no one else around, these boat-only snorkel spots are the way to go.
So if you’re ready to take the plunge, we’d love to show you the wild side of St. John on a private charter.
