Caminante boat docked in the middle of the sea one of the best Puerto Rico boat tours

13 Best Puerto Rico Boat Tours (By a Local)

As an island-hopping local, I highly recommend experiencing one (or a few!) of the best Puerto Rico boat tours.

Puerto Rico is an archipelago with hundreds of islands, cays, and mesmerizing bays, and the best way to experience it all is from the water. 

Whether you’re a sailing lover or a bonafide beach bum, you’ll fall in love with the island’s Caribbean coasts. So, to help you plan your most epic Puerto Rico itinerary, I’ve put together this list of top Puerto Rico boat tours. Let’s dive in!


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13 Best Boat Tours in Puerto Rico

Icacos Catamaran Day Sail

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

East Island boat docked near the shore with tourists swimming around
(Photo courtesy Viator / East Island Excursions)
  • Length: 6 Hours
  • 🌟 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.

Icacos is one of Puerto Rico’s offshore islands and is located off the shore of Fajardo. On this tour, crew members will provide you with snorkeling equipment so you can explore the coral reefs that surround Icacos. 

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

View of sailboats sailing in San Juan Bay at sunset
  • Length: 2 Hours
  • 🌟 Guest Reviews: 5/5 Stars
  • 🗺️ Highlights: Old San Juan, catamaran trip, San Juan Bay 
  • ✅ Includes: Beverages, rum punch, guide
  • 👉 Check prices & availability here

To balance out your Puerto Rico activities list, 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 the sunset and appreciate landmarks like El Morro and La Fortaleza during golden hour. You’re bound to enjoy an awesome time with family and friends and you’re free to bring your own food onboard.

Old San Juan Bay Sunset Sail

Revisit the 19th century while sailing the San Juan Bay topsail schooner

View of a boat tour in San Juan Bay at sunset
(Photo courtesy Viator / East Island Excursions)
  • Length: 2 Hours
  • 🌟 Guest Reviews: 4.5/5 Stars
  • 🗺️ Highlights: San Juan Bay, El Morro, La Fortaleza, sailing 
  • ✅ Includes: Guide, appetizers, beverages
  • 👉 Check prices & availability here

Sailing the San Juan harbor is an unforgettable experience, but doing so in a 19th-century-style vessel turns it up a notch. This tour takes you onboard the “Amazing Grace”, a 19th-century style topsail schooner. You’ll get to see top San Juan landmarks like La Fortaleza and El Morro from the bay.

Your tour guide will provide fun and unique insight information about Old San Juan while you enjoy light snacks and beverages. 

Couples will enjoy taking pictures in the afternoon light and seeing the sunset.

Culebra Day Trip by Catamaran from Fajardo

Snorkel for half a day in the breathtaking waters of Culebra

View of the sailing Catamarans on the clear blue water of Culebra
(Photo courtesy Viator / East Island Excursions)
  • Length: 6 Hours
  • 🌟 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 and Flamenco Beach. 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.

👉 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

Two people posing on the mini boat in San Juan
(Photo courtesy Viator / East Island Excursions)
  • Length: 1.5 Hours
  • 🌟 Guest Reviews: 4.5/5 Stars
  • 🗺️ Highlights: Mini boats, El Morro, San Cristobal Castle, Hato Rey
  • ✅ Includes: Life jackets, drinks
  • 👉 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.

Old San Juan Harbor Sailing Tour

Take a historical excursion through San Juan’s harbor onboard this 19th-century-style vessel

View of a boat with tourists in San Juan Bay
(Photo courtesy Viator / East Island Excursions)
  • Length: 1.5 Hours
  • 🌟 Guest Reviews: 4.5/5 Stars
  • 🗺️ Highlights: San Juan bay, El Morro, historic vessel 
  • ✅ Includes: Soft drinks, rum punch, historical capsules
  • 👉 Check prices & availability here

If you’re visiting the island on a cruise and need a short Puerto Rico excursion, then this is a great way to experience the San Juan harbor.

The Amazing Grace is a 19th-century style topsail schooner that will take travelers on a trip back in time while a knowledgeable guide gives capsules of history about the city. 

Both kids and adults can enjoy this one-hour and half-boat tour.

Sunset and Bio Bay at La Parguera

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

A boat docked near the boardwalk on Mata La Gata Island
Mata La Gata island
  • Length: 2 Hours
  • 🌟 Guest Reviews: 5/5 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. This boat tour takes you on a trip through La Parguera’s beautiful islands, cays, and bio bay.

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. 

To complete the experience, the captain will point out constellations with his laser and you will do some stargazing.

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

View of a sailing boat in Jobos Bay, Guayama on a sunny day
  • Length: 2 Hours
  • 🌟 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 boasts calm and clear waters and 15 cays worthy of a visit. 

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. 

San Juan 500-Year Anniversary Tour: See the City by Land and Sea

Explore San Juan from land and sea with this combined walking and boat tour

View of tourists inside the San Juan Harbor ride in San Juan Bay
(Photo courtesy Viator / Rico Sun Tours)
  • Length: 3.5 Hours
  • 🌟 Guest Reviews: 5/5 Stars
  • 🗺️ Highlights: El Morro, La Fortaleza, San Juan Bay, cruise tour 
  • ✅ Includes: El Morro entrance fee, walking tour, boat tour
  • 👉 Check prices & availability here

If you’re interested in learning all about Old San Juan, you don’t have to choose between exploring it by land or by sea. 

This tour allows you to visit the top attractions in San Juan on a walking tour and later revisit them on a boat tour from the bay. Best of all, it’s one of the top budget-friendly options to explore the bay.

One of the best highlights is getting a fully guided tour of Castillo San Felipe del Morro. Later from the boat, you’ll be able to appreciate the magnificent fortress from the outside, a view not everyone has seen.

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

View of a Catamaran in the tropical sea at sunset
  • Length: 5 Hours
  • 🌟 Guest Reviews: 5/5 Stars
  • 🗺️ Highlights: Fajardo, Cayo Piñero, Palomino, snorkeling 
  • ✅ Includes: Lunch, beverages, snacks, snorkeling equipment
  • 👉 Check prices & availability here

This tour takes you on a great day trip to Cayo Piñero, one of the hidden gems of the east coast. 

While most tours from Fajardo will take you to Icacos, this captain will take you to Cayo Piñero and Palomino. 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 Rainforest 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

View of bioluminescent plankton taken with long exposure at night
  • Length: 1 Hour
  • 🌟 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

A man holding a huge fish
  • Length: 4 Hours
  • 🌟 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 will take you to 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

View of Desecheo Island seen across the sea during sunset
Desecheo seen from Rincón

Snorkeling on Desecheo Island is one of the top things to do in Rincon. Located in the west of Puerto Rico, Desecheo is a paradise with high-visibility waters beaming with marine life. 

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. 

FAQs About Boat Tours in Puerto Rico

What are the best Puerto Rico boat tours?

The best boat tours in Puerto Rico are the boat tours to Icacos and Palomino. Other top Puerto Rico boat tours include La Parguera boat tours, Old San Juan boat tours, and boat tours to Culebra.

Is Puerto Rico a good place to sail to?

Puerto Rico is a good place to sail to all year round. Its coast boasts warm weather and the winds are between 10-15 knots on average. The waters are usually appropriate for beginners to expert sailors.

Do you need a passport to go to Puerto Rico by boat?

United States citizens don’t need a passport if they arrive in Puerto Rico by boat. Puerto Rico is a non-incorporated territory of the United States, so, US citizens can freely visit the island without a passport. However, it’s always recommended to carry your passport. 

Can you island hop from Puerto Rico?

Yes, travelers can go island hopping from Puerto Rico. The most popular islands on the east coast to hop to include Vieques, Culebra, Palomino, Icacos, and Culebrita. On the south coast, visitors like to go island hopping in La Parguera’s famous cays and islands including Cayo Mata La Gata, and Cayo Caracoles. It’s also possible to sail farther to the US Virgin islands.


Thanks for reading my guide on the top Puerto Rico boat tours! Now you can start preparing your Puerto Rico packing list to enjoy Puerto Rico’s top sites.

Have fun on Puerto Rico’s coasts!

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