El Nido Private Boat Lagoon Tours

Home » Palawan » El Nido Private Boat Lagoon Tours

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.

Kayaking through clear turquoise waters surrounded by limestone cliffs.

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, with our private tours 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. Feel free to send us a note or go ahead and book in our shopping cart:

book now button

Blank Form (#3)

You can also try our questionnaire for an instance quote and full customization of your tours.

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.

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.

Woman enjoying island hopping tour with limestone cliffs in the background.

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.

Woman kayaking in clear turquoise waters surrounded by limestone cliffs.

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.

El Nido limestone cliffs with turquoise waters and white sandy beach.

Beach with palm trees, soft white sand, and calm turquoise waters in the Philippines.

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.

Snorkeling with tropical fish during island hopping tour in the Philippines.

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.

Beach with turquoise waters, large rocks, and lush green cliffs in the background.

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.

Stunning island beach with turquoise waters, limestone cliffs, and palm trees in the Philippines.

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.

Tropical island with lush greenery, clear turquoise waters, and boats, perfect for island hopping ad.

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.

Scenic view of a cave entrance surrounded by rocky cliffs in the Philippines.

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.

Tropical cave entrance surrounded by rocky cliffs and lush vegetation in the Philippines.

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.

Scenic view of lush islands and clear waters in the Philippines.

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.

Scenic beach with boats, clear turquoise water, and lush green cliffs in the Philippines.

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.

Happy couple kayaking in clear blue waters in the Philippines.

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.

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!

Blank Form (#3)

You can also try our questionnaire for an instance quote and full customization of your tours.

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.

Sign for Sun Bar offering cold drinks, located under a palm tree at night.

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:

Blank Form (#3)

You can also try our questionnaire for an instance quote and full customization of your tours.

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

Scenic view of limestone cliffs reflected in calm river under blue sky.

Kayakers paddling in clear turquoise waters surrounded by lush cliffs in the Philippines.

Two people kayaking in clear turquoise waters near limestone cliffs in the Philippines.

Scenic view of limestone cliffs and turquoise waters in the Philippines.

Woman enjoying island hopping tour in the Philippines with turquoise waters and lush cliffs.

Stunning limestone cliffs and clear turquoise waters in the Philippines.

Scenic island cove with turquoise waters and boats, surrounded by lush cliffs.

Tropical island with a large rocky formation surrounded by clear blue water in Palawan, Philippines.

Young man enjoying a boat trip in El Nido's turquoise waters, Philippines.

Scenic view of turquoise waters and boats in a Philippine island cove surrounded by lush cliffs.

Clear turquoise lagoon with limestone cliffs and boaters in the Philippines.

Beautiful tropical island in the Philippines with vibrant turquoise waters and lush green cliffs.

Clear turquoise waters and rocky shoreline in the Philippines.

Unique limestone formations and boats at a Philippine beach.

Stunning island landscape with turquoise waters and lush cliffs in the Philippines.

Beautiful tropical river surrounded by lush greenery in the Philippines.

Two women exploring a cave with water, wearing life jackets, in the Philippines.

Kayakers enjoying turquoise waters surrounded by limestone cliffs in the Philippines.

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.

Booking

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

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.

Blank Form (#3)

You can also try our questionnaire for an instance quote and full customization of your tours.

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

Frequently asked questions

Tour A focuses on the Big Lagoon and Small Lagoon in Miniloc Island, as well as Shimizu Island, Secret Lagoon, and a white sand beach stop. It is the most popular tour and ideal for first-time visitors.

Tour C includes Secret Beach, Hidden Beach, Matinloc Shrine, Star Beach, and Helicopter Island. It is known for beautiful snorkeling spots and scenic rock formations.

Tour C is considered the best for snorkeling due to its clear waters and coral gardens, especially around Star Beach and Helicopter Island. Tour A also includes good snorkeling spots.

It is not recommended to combine tours in one day because each one takes nearly a full day. Private tours may allow partial combinations, but most travelers book multiple days to enjoy each destination fully.

Joiner tours are shared with other travelers and follow a fixed itinerary. Private tours are more expensive but allow flexible schedules, customized stops, and a more exclusive experience.

Joiner tours typically cost 1,200 to 1,400 per person for Tours A and C. Private tours start from around 15,000 for 2 people (price depends on number of people), depending on the tour package and boat type.

Most joiner tours include entrance fees, but it is important to confirm. Our private tours always include entrance fees and lunch. You also need to pay a 200 Eco-Tourism Development Fee (ETDF), valid for 10 days, which is sometimes not included in the package.

Bring swimwear, sunscreen, towel, dry bag, water, snacks, waterproof phone case, while snorkeling gear is included. Lunch is also included. 

The best time is during the dry season from November to May. December to March usually offers the calmest sea conditions and clearest water for snorkeling and kayaking.

It is recommended to book in advance, especially during peak months from December to April. Private tours in particular can fill up quickly due to limited boats with lagoon permits.

Important links and related tours

Private multiday expedition tours between El Nido and Coron
Group multiday joiner 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

Our reviews:

Screen Shot 2025 03 07 at 11.53.40 AM
Screen Shot 2025 03 07 at 11.53.40 AM
previous arrow
next arrow

Check out our latest google reviews!

Facebook reviews
Home » Palawan » El Nido Private Boat Lagoon Tours

Submit your review
1
2
3
4
5
Submit
     
Cancel

Create your own review
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!