El Nido Private Boat Lagoon Tours

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A person kayaking in clear turquoise waters of El Nido, surrounded by tall rocky cliffs and lush greenery under a bright blue sky, offers a breathtaking boat tour experience.

Go against the current of the crowd by visiting the famous El Nido lagoons in a private tour when the others are not present. Or we can organise group tours for you as well.

Where should I go in the Philippines? This question has been asked a million of times whenever someone for the first time is visiting Philippines and has no idea where to go. If you are the kind of person who visits google whenever you are planning your trip for the first time, Palawan is at the top. In Palawan, El Nido and Coron are the most visited places.

El Nido has been one of the most popular destinations for tourists visiting Palawan because of its beautiful lagoons and secret beaches. The El Nido lagoons are some of the nicest scenery in the Philippines, if not the world. But having been discovered long enough ago, they have become inundated with the usual swarms of tourists bobbing in their obnoxious coloured life preservers.

If you would like a slightly different approach, we offer an opposite route, so you have a better chance of enjoying an entire lagoon for your small crew alone and avoid the crowds. This is possible by booking a private boat tour with us.

Experience the tranquility of a boat tour in El Nido, with calm waters mirroring the blue sky and clouds. Text reads "BOOK TOUR NOW.
There are three famous tours in El Nido. You can choose between Tour A, Tour B, Tour C and Tour D. Prices depend on the tour and number of people.

Which is the best tour in El Nido?

If you have a limited number of days in El Nido, of course you want to choose the best tour. When I first went to El Nido a few years ago, I stayed for one week, during which time I accomplished Tours A, B and C. Following is my experience regarding these tours to help you choose which one best suits your tastes and time.

El Nido Private Boat Tour A

For first timers who want to experience the beauty of El Nido in one fell swoop, Tour A is PERFECT for you. If you only have time to take one tour, Tour A is the answer because it best showcases what El Nido is all about: snorkeling or swimming in peaceful blue clear waters while surrounded by a jaw-dropping view. (Prices at the bottom.)

Big Lagoon

This is an easy first stop since you can simply opt to marvel at the view that will serve to prepare you for the beauty that is Small Lagoon.

In El Nido, a woman in a bikini sits on a boat during a captivating tour, gazing at towering limestone cliffs covered with lush greenery over the turquoise sea.

Small Lagoon

This is a gorgeous little corner of El Nido that can be accessed by kayaking or swimming through a gap between limestone formations. Pictures won’t suffice since you have to see it yourself to understand why Small Lagoon is a favorite pit stop among travelers to El Nido.

A person smiling on a yellow kayak in the clear turquoise waters of El Nido, surrounded by fellow kayakers and rugged rocky cliffs, offers an unforgettable boat tour experience.

Secret Lagoon

This is accessible via a hole through a rock. The water in the lagoon is a cool blue, which is a striking contrast for the usual emerald waters found throughout El Nido.

Aerial view of a tropical beach in El Nido with clear turquoise water, rocky cliffs, and lush greenery. People are relaxing on the white sandy shore while a boat tour glides nearby.

Aerial view of a tranquil El Nido beach with clear water, a boat from the local tour gliding peacefully, a few people onshore, and palm tree shadows casting on the sand.

Advin Dive site

This is one of the most popular dive sites in El Nido and known for hard corals, sea turtles, and barracuda. A must for big snorkeling fans!

Shimizu Island

If there’s one thing you have to do at Shimizu Island, it’s to snorkel! The waters are fairly shallow, but you’ll get to see schools of fishes while swimming through the emerald and turquoise waters. It’s also a good spot for picnic lunches or just lazing around.

A split-view photo captures a boat tour gliding above and vibrant striped fish swimming in the clear blue waters below, with El Nido's stunning tropical island scenery in the background.

South Entalula

This is a dive and snorkeling site known for its beautiful soft corals, whip corals and sea fans.

Seven Commandos Beach

This is perfect for families who want a little bit of everything that the beach can offer. There’s a dedicated swimming area for swimmers, you can kayak and enjoy the peaceful waves, or you can lounge around with a drink or Halo-Halo (a Filipino delicacy of crushed ice with fruits and condensed milk) in hand. Papaya Beach is adjacent to Seven Commandos Beach and it’s a great beach if you want peace and quiet.

A small beach in El Nido with tourists on white sand, surrounded by rocky cliffs covered in lush green vegetation, offers an inviting scene. A red boat on the water hints at the possibility of an adventurous boat tour.

Take note: Before, you can technically visit both the Small and Big Lagoon in the same tour, but because of an increasing number of tourists visiting these lagoons, the government decided to limit the number of tourists visiting each lagoon at any one time. Hence, you can only choose which one you would like to visit, the Small or Big Lagoon, in any single day.

El Nido Private Boat Tour B

For those who are more into caves and coves, Tour B is perfect for you. Be mesmerized by these amazing wonders of El Nido. (Prices at the bottom.)

Pinagbuyutan Island

  • Snake Island
  • Entalula Island
  • Cudugnon Cave
  • Cathedral Cave

Pinagbuyutan Island

This is home to one of the best beaches in the Philippines. Witness sparkling clear waters in varying shades of blue, enjoy the shade of coconut trees lining the sand, fresh coconut juice, and wonder at the towering cliffs that complete the view.

Aerial view of El Nido's tropical beach with clear turquoise water, rocky cliffs, lush palm trees, and boats ready for an unforgettable boat tour.

Snake Island

This is so named because the sandbar, when viewed from above, resembles a snake. Do not be afraid, though, there aren’t any snakes aroundd here. It is better to come early when it is low tide so that you can see the long white sand bar. If you want to see mangroves, a quick walk to a different part of the island will reward you with a view of the gorgeous mangroves that dot the fine sand.

Scenic view of El Nido's bay with clear turquoise water, small boats awaiting a boat tour against the backdrop of lush green hills and a partly cloudy sky.

Entalula Island

This is an idyllic spot that’s perfect for families or beach lovers who want to enjoy clear waters and fine sand, which most people say are better than on Boracay Beach. A must-experience pit stop!

Cudugnon Cave

To enter Cudugnon Cave you need to go through a hole that barely fits an adult. Inside you’ll find multi-color walls and bats. A stint at Cudugnon Cave definitely makes for a thrilling experience.

The limestone cave entrance by the water, surrounded by rugged rock formations and patches of green foliage, awaits explorers on an El Nido boat tour.

Cathedral Cave

This is a massive structure in varying shades of black, white and gray. You can enter the cave by swimming or you can do so without disembarking from your boat. It’s an awesome pit stop in that you can really see nature at work here. The interior of the cave does resemble a cathedral and it’s a solemn place that will instill you with a renewed sense of wonder for all that Nature has to offer.

The rocky cliff with a cave opening, surrounded by lush greenery, stands majestically beside the clear blue waters of El Nido. Under a partly cloudy sky, this stunning view is best experienced on an adventurous boat tour.

El Nido Private Boat Tour C (Hidden beaches and Shrines)

Trust me, it’s paradise. This is where the hungry come to feed. For mine is the generation that travels the globe and searches for something we haven’t tried before.”
-Alex Garland, The Beach

If you have an appetite for discovery, Tour C is for you. Like a good story, we’ll begin with an eye opening scene: Cadlao Lagoon. Next you’ll get hooked in by Talisay Beach, feel a rush of excitement at Secret Beach, and end on a tranquil note at Seven Commandos. Incidentally, the novel The Beach by Alex Garland was said to be partly inspired by Secret Beach, the fifth stop in our itinerary. (Prices at the bottom.)

Cadlao Lagoon

It‘s emerald waters and towering limestones make this place picturesque and amazing.

Helicopter Island

Looks exactly like that from a distance – a helicopter except without the propeller. Helicopter Island is home to excellent diving spots and it’s easy to lose track of time just gazing at the emerald waters. Depending on the weather conditions, our tour guides will tell you when the waves are too rough and could prove to be unsafe for snorkelers.

Aerial view of small, lush green islands with rocky cliffs surrounded by calm blue water, perfect for an El Nido boat tour.

Talisay Beach

This is our usual lunch stop and only a few minutes away from Matinloc Shrine. It is also a great destination for snorkeling and diving.

Wooden boats are docked on El Nido's clear turquoise shore, where lush greenery and rocky cliffs create a stunning backdrop. People enjoy swimming and lounging, making the most of this idyllic spot, while others embark on a memorable boat tour.

Secret Beach

Massive limestone formations will hide the beach from view, hence the nickname Secret Beach. There are two ways to visit the island: via boat or via a small crevice. If you can swim and would love to feel a rush of excitement upon discovering a secluded beach, then swimming is the way to go.

Seven Commandos Beach

A perfect for families who want a little bit of everything the beach can offer. There’s a dedicated swimming area for swimmers, you can kayak and enjoy the peaceful waves, or you can lounge around with a drink or Halo-Halo (a Filipino delicacy of crushed ice with fruits and condensed milk) in hand. Papaya Beach is adjacent to Seven Commandos Beach and it’s a great beach if you want peace and quiet.

A smiling woman and man enjoy a kayaking adventure on a sunny day, navigating the clear blue waters of El Nido. They are surrounded by lush greenery and rocky cliffs, creating a picturesque backdrop for their unforgettable boat tour.

El Nido Private Tour D

Not as popular a choice but here it is nevertheless:

1 . Small lagoon
2. Cadlao lagoon
3. Pasandigan beach
4. Nat Nat beach
5. Paradise beach

More details here and prices listed below.

El Nido A&C Combo tour

1 . Small lagoon
2. Secret lagoon
3. Hidden beach/secret beach
4. Talisay beach
5. Helicopter island

More details here.

Custom day tour

Not a problem to whip up something different, such as picking you up and dropping you off at your resort island, or any other option which suits your fancy. Just send us a note and we’ll figure something out!

So which choice?

After doing tours A, B and C, I liked Boat Tour A the most. The best part for me was the lagoon. In the Small Lagoon I rented a kayak and shared it with a friend. You will be cruising on clear waters until you make yourself fit in a small hole in order to enter the other side of the lagoon. You may skip the kayak and just snorkel if you so choose, but be careful of the jellyfish which might appear sometimes.

A sign reading "Sun Bar: We serve cold drinks here as cold as your ex" is attached to a palm tree at night, perfect for those returning from an El Nido boat tour.

El Nido is a nice place to stay if you want some adventures and night life. There are plenty of bars along the beach in town. Our favorite bar is Pukka bar as they play live music every evening, most especially reggae music. If you are tired from island hopping, you can chill and work on your sun tan and beach bumming in Las Cabanas beach. If you are looking for some adventures, you can do zip lining there as well. Las Cabanas beach for me is the perfect place to have a beer while watching the sun set.

A person is relaxing on a hammock by a tropical beach in El Nido, with mountains and a boat tour gliding through the background.
A person swings from a tree over a sandy beach, with the picturesque El Nido island gracing the background, as if inviting them to explore its beauty through a serene boat tour.

Three beach chairs facing a calm sea at sunset, with scattered clouds and distant islands reminiscent of an El Nido boat tour on the horizon.

If you want a more quiet place and longer beach, Nacpan beach is a nice place to visit. If you know how to ride a motorbike, it is cheaper to rent one for 350-400pesos, or charter a tricycle if there are more than two of you.

Tropical beach with palm trees, sandy shore, and calm sea under a cloudy sky, surrounded by green hills; perfect for an El Nido boat tour.

As what I have previously mentioned, Coron is also one of the famous spots tourists love to visit in Palawan. It is known for shipwrecks during the Japanese World War II and thus makes it great for diving. If you are not into diving, there are islands with  beautiful sand bars perfect for beach bumming, and sites plentiful of corals and fishes perfect for snorkeling.

A snorkeler glides above a submerged shipwreck in the crystal-clear waters of El Nido, as part of an unforgettable boat tour experience.
One of the eight shipwrecks in Coron, Palawan

Because there are so many things to do and see in Coron, crowds are increasing and can be a pain in the butt if you want to enjoy the beaches and lagoons just for yourselves. That’s why we have figured out a hack on how to avoid the crowds and enjoy the beaches just for yourselves. For customized private boat tours in Coron only, or multiday tours between Coron and El Nido, contact us here or through the photo below:

Aerial view of a boat on crystal-clear water near a sandy beach in El Nido. Text reads "Palawan boat tours.
Enjoy your bobbing!

Back to itinerary travel suggestions for Palawan

A bunch of pics

Experience the scenic view of limestone cliffs reflected in tranquil blue water under a bright sky with fluffy clouds during an El Nido boat tour.

Kayakers in yellow canoes paddle through the clear turquoise waters of El Nido, surrounded by rocky cliffs and lush greenery, as if on a picturesque boat tour.

Two people kayaking on clear turquoise water surrounded by rocky cliffs and lush greenery, reminiscent of an idyllic boat tour in El Nido.

People swimming in clear turquoise waters, surrounded by the tall limestone cliffs and lush greenery of El Nido, under a bright blue sky—a perfect day for a scenic boat tour.

On a boat tour in El Nido, a woman gazes at vibrant turquoise waters and lush, rocky cliffs under a bright blue sky.

A traditional boat glides on the turquoise waters of El Nido, framed by tall, jagged limestone cliffs under a clear blue sky.

Aerial view of a turquoise lagoon in El Nido, surrounded by rocky cliffs, with several small boats on a scenic boat tour gliding across the water.

A large, lush rock island rises from the vibrant blue waters under a clear sky in El Nido, where a boat tour offers an unforgettable experience.

Person in a red shirt sitting on a boat, navigating clear turquoise waters surrounded by rocky cliffs. Text: "El Nido Day Trip A – the ultimate boat tour adventure.

Aerial view of a turquoise lagoon in El Nido, surrounded by rocky cliffs with several boats from a boat tour gracefully floating on the water.

A scenic view of a turquoise lagoon with rock formations, a boat carrying passengers on an El Nido boat tour, and a person kayaking near the shore under a clear sky.

Experience the vibrant tropical seascape of El Nido with turquoise waters, lush green islands, and a boat's outrigger in the foreground—perfect for an unforgettable boat tour.

Discover a serene tropical lagoon on an El Nido boat tour, where crystal-clear turquoise water meets rocky cliffs and lush greenery under a bright blue sky.

A wooden boat from an El Nido boat tour is moored near a large, jagged rock formation on a sandy shore, with clear blue skies in the background.

Aerial view of turquoise waters, rocky cliffs, and lush green islands in a tropical landscape, perfect for an El Nido boat tour adventure.

A tranquil river surrounded by lush green cliffs and trees reflects in the clear water under a bright sky, reminiscent of an El Nido boat tour.

People wearing life jackets and snorkeling gear explore a cave partially submerged in water, all part of an unforgettable boat tour in El Nido.

People kayaking on the clear blue waters of El Nido, surrounded by rocky cliffs and lush greenery under a bright sky.

El Nido's clear turquoise waters welcome you to explore their beauty, as boats near rocky cliffs and lush green vegetation glide under a brilliant blue sky. Embark on a captivating boat tour to witness this stunning scenery firsthand.

Two people kayaking in a vibrant green lagoon surrounded by lush cliffs in Small Lagoon, El Nido, experience the beauty of this paradise often explored on a boat tour.

Prices and rates

Includes entrance fees, environmental fee, licensed tour guide, lunch and snorkel gear.

A table displaying prices for El Nido tours A, B, C, and D, based on the number of participants for boat tours, ranging from 2 to 12 with varying costs.

If you are interested in booking with us, or for more information, simply send us a note and we’ll be happy to oblige. We are continually expanding our services and have travelled extensively throughout the country, happy to help you plan your visit here, no matter where it is.

Aerial view of a boat cruising on clear turquoise water near a sandy beach in El Nido. Text reads "Palawan boat tours.Experience the thrill of island hopping in the Philippines

Important links and related tours

Private and group multiday expedition tours between El Nido and Coron
Private boat tours around Coron
Combination El Nido and/or Coron boat tours with multiday expedition in between
Marriage proposal tours

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Island Hopping in the Philippines
Average rating:  
 2 reviews
 by Gérard BENOIT
An excellent memory

I was looking for a personalized excursion to the beautiful Gulf of Bacuit.

Seeing the comments, I contacted Mel.

Very responsive, very efficient and perfect organization.

The flight attendants were very friendly and very helpful.

And I'm not even talking about the meal on board...a marvel.

In all fairness, this excursion will remain an excellent memory and I cannot recommend Mel and his team highly enough.

A big thank-you.

 by Karel
What an awesome area!

If you want exotic, this is a cool place to go!