13 Best Puerto Rico Boat Tours (By a Local)

Icacos Catamaran Day Sail

Snorkel among coral reefs in a spot where dolphins have been known to hang out.

• ⌚ Length: 6 Hours
• 📍 Departs from: Puerto del Rey Harbor, Fajardo
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Icacos Island, snorkeling, beach
• ✅ Includes: Snorkeling gear, lunch, rum cocktails
• 👉 Check prices & availability here

The Icacos Island catamaran trip is one of the most popular Puerto Rico activities, not only for its clear turquoise beaches, but also for the party atmosphere among beachgoers.

One of Puerto Rico’s offshore islands, Icacos is located off the shore of Fajardo. On this tour, crew members will provide you with snorkeling gear so you can adventure on your own and explore Icacos’s surrounding coral reefs.

The relatively shallow waters are ideal for visiting with the family. Your trip also includes lunch and beverages, so you only need to pack a quick-drying towel, and the will to enjoy one of the best snorkeling trips you’ll ever experience.

San Juan Catamaran Sunset Sail with Drinks Included

Board a luxury catamaran and enjoy San Juan’s mesmerizing sunset out on the bay.

• ⌚ Length: 2 Hours
• 📍 Departs from: San Juan Bay Marina
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Old San Juan, catamaran trip, San Juan Bay 
• ✅ Includes: Beverages, rum punch, guide
• 👉 Check prices & availability here

You don’t have to leave the capital city to enjoy a great boat tour. If your Puerto Rico activities list is all based in San Juan, this catamaran trip allows you to pause, relax, and admire the sunset from San Juan Bay.

With an open bar and a professional captain, travelers will sail out to the bay during sunset and appreciate landmarks like El Morro and La Fortaleza during golden hour. 

I recommend taking this tour with family or friends for an even better experience! You’re welcome to bring your own food and drinks on board, so don’t forget to pack your favorites.

Culebra Day Trip by Catamaran from Fajardo

Snorkel for half a day in the breathtaking waters of Culebra.

• ⌚ Length: 6 Hours
• 📍 Departs from: Puerto Marina del Rey, Fajardo
• 🌟 Guest Reviews: 4.5/5 Stars
• 🗺️ Highlights: Flamenco Beach, Culebrita, snorkeling
• ✅ Includes: Life jackets, lunch, drinks, snorkeling gear
• 👉 Check prices & availability here

Culebra’s beaches are indeed some of the best beaches in Puerto Rico, and this is one of the few boat tours that will take you to them directly from the main island. 

With these tours, you’ll get to snorkel in the waters of Playa Carlos Rosario, Flamenco Beach or Cayo Luis Peña. These white sand beaches are known for their reefs and clear waters and are easily two of the top spots for snorkeling in Puerto Rico.

Between stops, you will enjoy a buffet lunch. You can also sip on cocktails and enjoy dessert.

If this tour isn’t right for you, I’ve also got a whole guide listing more day trip tours to Culebra.

👉 Tip: Keep in mind visiting Culebra island is subject to weather conditions. If the sea is too choppy, the crew might opt for visiting Cayo Luis Peña or Icacos instead.

San Juan Mini Boats

A fun and exciting way to see Old San Juan’s highlights while driving yourself on the boat.

• ⌚ Length: 1.5 Hours
• 📍 Departs from: San Juan Bay Marina, San Juan
• 🌟 Guest Reviews: 4.5/5 Stars
• 🗺️ Highlights: Mini boats, El Morro, San Cristobal Castle, Hato Rey
• ✅ Includes: Life jackets, drinks, use of mini boat
• 👉 Check prices & availability here

If you’re looking for a private boat tour instead of a catamaran trip, then this mini-boat experience is an ideal option. With an hour and a half on the water, travelers will get to ride this mini boat around San Juan Bay to see Old San Juan, El Morro, and even San Juan’s commercial port in Hato Rey.

During your stops, local guides will highlight the best of San Juan’s history and pinpoint the local flora and fauna.

La Parguera Sunset Private Boat Tour

Take a boat ride to an offshore island and then stop at one of Puerto Rico’s bio bays.

• ⌚ Length: 2 Hours
• 📍 Departs from: (Location or write details of hotel pickup per tour page)
• 🌟 Guest Reviews: 4/5 Stars
• 🗺️ Highlights: La Parguera Bio Bay, Mata La Gata Island, Cayo Caracoles 
• ✅ Includes: Life jackets, beverages, guided tour, stargazing
• 👉 Check prices & availability here

Puerto Rico bio bays promise an unforgettable experience for travelers, and if you’re going to splurge on something in Puerto Rico, it should definitely be a boat tour to see this natural wonder. 

After enjoying a memorable ride between La Parguera’s “floating houses,” you’ll make a stop at Mata La Gata, an island with a natural pool, where you’ll have an amazing time swimming until sunset. 

After, you’ll take a boat ride to La Parguera bio bay, where the crew members will explain how the unique phenomenon of bioluminescence works and you’ll be able to jump in the glowing water. 

Best of all, this private tour guarantees a small group, so you can fully enjoy your experience.

Private Sunset Sail – South Coast of Puerto Rico

Admire Jobos Bay in the south of Puerto Rico in this boat tour with a small group of six people.

• ⌚ Length: 2 Hours
• 📍 Departs from: Fishing Club, Guayama
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Jobos Bay, Salinas, Guayama 
• ✅ Includes: Snorkeling equipment 
• 👉 Check prices & availability here

This boat tour takes you to Jobos Bay National Estuarine Research Reserve in the south of Puerto Rico. Considered one of the best things to do on the island, Jobos Bay is a reserve where, as a nature enthusiast, you’ll enjoy the 15 cays worthy of a visit and their wildlife.

The reefs in the nature reserve make this water perfect for snorkeling and diving. On this private tour, you’ll get to enjoy the best of Jobos Bay with a small group of six people and without the crowds typical of Icacos island. 

Janise Sailing & Snorkeling Day Charter in Fajardo, Puerto Rico

This small group private tour will take you on a day trip to the relaxing Cayo Piñero.

• ⌚ Length: 5 Hours
• 📍 Departs from: Puerto del Rey Marina, Fajardo
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Fajardo, Cayo Piñero, Palomino, snorkeling 
• ✅ Includes: Lunch, beverages, snacks, snorkeling equipment
• 👉 Check prices & availability here

While Icacos is a preferred destination on the East Coast, it’s also true that it can get pretty crowded. This tour takes you on a great day trip to Cayo Piñero, a gem that even many locals are unaware of. 

You’ll also stop at Palomino, a smaller cay. Both islands are less frequented and are an hour away from the coast.

Your group will meet in the morning at Puerto Del Rey Marina in Fajardo and, as you sail away, you’ll get the chance to appreciate the El Yunque National Forest from a distance.

You’ll receive snorkeling equipment to explore the Caribbean waters, but make sure to bring your own water shoes. The VIFUUR water shoes are breathable, quick-drying, and comfortable for doing water sports or just walking on the beach. 

Vieques: Bioluminescent Bay Boat Tour

This boat tour allows travelers to enjoy Mosquito Bay, the brightest bio bay in the world.

• ⌚ Length: 1 Hour
• 📍 Departs from: Sun Bay Beach, Vieques
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Vieques, Mosquito Bay, bio bay 
• ✅ Includes: Transportation from Esperanza to the bay
• 👉 Check prices & availability here

Vieques is home to one of the top hidden gems in Puerto Rico, Mosquito Bio Bay, one of three bio bays in Puerto Rico. Considered the brightest bio bay in the world, seeing this bio bay for yourself is one of the top Vieques activities.

Although most tours to the bio bay are by kayak, this boat tour allows you to see the beauty of the bio bay without worrying about anything else. You’ll also get to explore different parts of the bay to see how the bioluminescence changes. 

Another great part of this boat tour is that you can take photos freely without worrying about your kayak tipping over.

Light Tackle Tarpon & Snook Fishing Charter

This tour not only will take you to enjoy Puerto Rico’s coasts, but also you’ll get to go fishing for tarpon.

• ⌚ Length: 4 Hours
• 📍 Departs from: Cooperativa de Pescadores Ramp, Loíza
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Laguna San José, Laguna Torrecilla, tarpon fishing 
• ✅ Includes: Drinks, fishing equipment, baits
• 👉 Check prices & availability here

If you’re a fishing enthusiast, then you’ll be glad to know this boat tour can take you fishing to some of the most popular spots in Puerto Rico.

Puerto Rico waters are great for fishing tarpon, sea bass, jack, and snook. This 4-hour tour navigates the San José and Torrecilla lagoons on the north coast, where these species are abundant.

Desecheo Island Charter

Take a tour to a “forbidden island” where the waters have high visibility and dive in them without a certification.

• ⌚ Length: 6 Hours
• 📍 Departs from: Black Eagle Marina, Rincon
• 🌟 Guest Reviews: 4/5 Stars
• 🗺️ Highlights: Desecheo Island, snorkeling, diving 
• ✅ Includes: Beverages and snacks
• 👉 Check prices & availability here

Snorkeling on Desecheo Island is one of the top things to do in Rincon. Located outside Puerto Rico’s west coast, Desecheo is a paradise with coral reefs so colorful, they are known as Candyland. 

It also has numerous underwater caves and rocky shelters with abundant marine life that makes it hard to believe it was once used as a bombing range by the United States Armed Forces.

This half-a-day excursion allows you to explore the underwater caves, snorkel around coral reefs, and enjoy a relaxing day while admiring this “forbidden island”.

During the winter season, you might get to spot whales during your trip. 

👉 Local Tip: Call ahead before booking your tour.

Public Culebra Power Boat Snorkeling & Beach Tour

Escape to Puerto Rico’s most renowned beaches.

• ⌚ Length: 6 Hours
• 📍 Departs from: M-21 Villa Marina Yacht Harbor, Fajardo
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Culebra, Flamenco beach, snorkeling 
• ✅ Includes: Lunch, all-day beverages, snorkeling gear, flotation devices
• 👉 Check prices & availability here

Culebra is one of the most sought after destinations in Puerto Rico, and as a beach lover, I can tell you, it’s totally worth the hype. 

Culebra’s beaches offer clear turquoise waters and you can easily explore them with this boat tour.

Unlike most popular Puerto Rico boat tours, this tour visits Flamenco Beach directly (as long as the weather and ocean conditions allow it), which means you can skip the hassle of the crowded public ferry.

Prepare to snap some photo card worthy pictures, specially at the infamous Flamenco Beach tank. Your tour also includes snorkeling gear and flotation devices, so you can freely explore the local reefs.

Your lunch is also included, so all you have to pack is your swimwear, sunblock, and will to have fun!

Nite Snorkeling and Boat Experience

Sail after dark to explore Puerto Rico’s night underwater world.

• ⌚ Length: 3 Hours
• 📍 Departs from: Villa Marina Yacht Harbor, Fajardo
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Sunset, night snorkeling, stargazing 
• ✅ Includes: Snorkeling gear, waterproof light, charcuterie board, non-alcoholic drinks, marine-life identification card
• 👉 Check prices & availability here

Not many boat excursions in Puerto Rico take place after dark, but this sailing adventure in Fajardo starts the fun right after sunset! If you’re looking for a different kind of boat tour I absolutely recommend taking this night snorkeling excursion with Pirate Snorkeling Shack. 

You’ll sail off Fajardo at sunset, with the golden hour painting some of the east coast’s main landmarks, including El Yunque and Cabezas de San Juan Nature Reserve. You’ll later arrive at Palomino island, where your instructor will guide you through the local reefs where you’ll appreciate how marine life comes alive at night.

And if that wasn’t magical enough, after an hour on the water, you’ll get back on board to enjoy snacks under an unpolluted sky.

Aguadilla Weekend Sunset Tours

Hop through Aguadilla’s beaches during the magic hour.

• ⌚ Length: 3 Hours
• 📍 Departs from: Crashboat Experiences, Aguadilla
• 🌟 Guest Reviews: 5/5 Stars
• 🗺️ Highlights: Sunset, beach hopping, snorkeling 
• ✅ Includes: Drinks, towels, snorkeling gear
• 👉 Check prices & availability here

The west coast offers the best sunsets in Puerto Rico, and this tour allows you to combine them with a sail through Aguadilla’s beautiful coast.

You’ll navigate through Aguadilla’s Bay while hearing all about the town’s history and formation. You’ll see popular landmarks like the Aguadilla old sugar cane pier and stop and multiple beaches where you can go snorkeling. 

Alternatively, you can just soak in the sun and feel the breeze with a drink in hand.