Best overwater bungalows in the Philippines

It’s no secret that the Philippines is a tropical paradise. Millions of travelers visit the archipelago every year in search of spectacular beaches where the crystal-clear waters take center stage. If your Philippines travel itinerary calls for a once-in-a-lifetime treat—staying in one of those epic villas or cabins where you feel like you’re floating right over the water—don’t worry, you can absolutely make it happen. In this article, we’re going to show you the best overwater villas and bungalows in the Philippines.

Beyond the impressive resorts, luxury hotels, and backpacker hostels, the Philippines’ 7,000+ islands are also home to stunning overwater stays that rival the famous spots in the Maldives or French Polynesia. They’re typically built from wood and topped with the country’s traditional thatched or nipa roofs, but that doesn’t mean you’ll have to give up any modern comforts—in many cases, you’ll even get your own pool or jacuzzi with sweeping ocean views.

Important things to know about overwater villas in the Philippines

One crucial factor when choosing this type of accommodation is location. While location matters wherever you stay, since you’re splurging a bit more than usual here, you’ll want it to be somewhere special, right? As you’ll see below, many of these overwater villas in the Philippines are located in or around El Nido. In our opinion, this is the best area for this kind of stay, as the landscapes you’ll see right from your cabin are spectacular. When you wake up, you’ll be greeted by towering dark limestone cliffs rising straight out of turquoise water.

Speaking of El Nido specifically, these overwater hotels are located on private islands, so you might be wondering how to get there. Don’t sweat the logistics—almost all of them, if not all, include boat transfers from El Nido Airport at Lio Beach.

Also, since these resorts are in secluded locations and it’s not exactly practical to leave every time you want to eat, many offer full-board packages or, at the very least, breakfast. Of course, they also have restaurants for à la carte dining. On top of that, many have exclusive spas, plus kayaks, paddleboards, and other activities. In El Nido, almost all resorts include 1 or 2 island-hopping tours in the room rate, depending on the length of your stay.

If you are planning a honeymoon in the Philippines, don’t hesitate to mention it when booking, as they always have a little perk for newlyweds. If you’d like to have a special ceremony or even a full wedding in the Philippines—which you can later legalize back home—that can also be arranged for you. Imagine saying “I do” in such a heavenly setting.

Without further ado, let’s introduce you to the best overwater villas in the Philippines.

Comparison of hotels with overwater bungalows in the Philippines

In this table, you can quickly compare the overwater villas we’ve selected in the Philippines. We thought it was important to highlight the location, and price.

RESORTS WITH OVERWATER BUNGALOWS IN THE PHILIPPINES	AREA	PRICE/NIGHT
El Nido Resorts Miniloc Island	El Nido	From $712
El Nido Resorts Apulit Island	El Nido	From $576
El Nido Resorts Lagen Island	El Nido	From $680
Huma Island Resort and Spa	Coron	From $880
Paolyn Floating House	Coron	From $480
Pearl Farm Beach Resort	Davao	From $384
Club Tara Resort	Surigao	From $78

The best overwater bungalows in the Philippines

Let’s take a look at these places one by one. Check out the photos—you’re going to be amazed! You can probably already picture yourself there, relaxing in your very own overwater villa in the Philippines.

$$$ El Nido Resorts Miniloc Island

El Nido Resorts is one of the top hotel groups in the Philippines, with several beautiful properties scattered around Palawan. The first one on our list is located on Miniloc Island, home to El Nido’s most famous lagoons: Small Lagoon and Big Lagoon. This means you’ll be in a stunning setting, with the chance to explore by kayak or paddleboard on your own before the crowds arrive. It truly is one of the best resorts in El Nido.

The service is exactly what you’d expect from a 5-star hotel, and to top it all off, impressive island-hopping tours are included in the room rate. You also have the option to snorkel at nearby reefs or visit the spectacular Entalula Beach, one of our personal favorites.

You can choose from the following types of rooms:

• 7 Water Cottages: Since you’re hunting for overwater bungalows in the Philippines, this should be your pick. These beautiful bungalows feature the archipelago’s traditional roofline, a double bed, and a small balcony.
• 5 Deluxe Seaview Rooms: Charming rooms for up to 3 adults with direct views of the water and a small balcony to sit and soak it all in. Fun fact: the electricity in these rooms comes directly from solar panels.
• 5 Seaview Rooms: If you’re traveling as a family, this is a great option. A two-story room with a double bed downstairs and two single beds upstairs. Of course, it also boasts wonderful direct sea views.
• 2 Family Garden Cottages: These are the most economical since they don’t have sea views, but they are lovely, spacious bungalows for up to 3 people just a few steps from the beach.
• 3 Cliff Cottages: Located at the highest point of the resort and offering gorgeous panoramic views, these are two-story cottages for 4 people.
• 12 Beachfront Cottages: With room for up to 3 guests, this is the choice if you want to be right on the sand.

When hunger strikes, you can head to the bar or restaurant, but if it’s a special occasion, they can also arrange private dinners on the beach. Other resort facilities include a gym, clinic, boutique, spa, and dive center, as well as a beautiful infinity pool. All in all, it’s a 10/10 hotel in a dream location. And if you don’t believe us, check out this 3D animation.

Click here to check out the overwater villas

$$$ El Nido Resorts Apulit Island

The most affordable hotel in the El Nido Resorts group isn’t actually in El Nido proper, but it still delivers that overwater bungalow experience in the Philippines you’re looking for.

It’s on Apulit Island, a private island in Taytay Bay, on the opposite side of Palawan from El Nido and about 40–50 minutes from the mainland. Because of this, getting there takes a bit more effort, and the standard El Nido island-hopping excursions aren’t offered here. That doesn’t mean there’s nothing to do, though—in fact, the snorkeling is fantastic and includes a sunken Japanese ship and a giant clam sanctuary. You can also climb dramatic limestone cliffs, explore caves, and visit a beautiful spot called White Island that you’re sure to fall in love with. In fact, this resort has the highest rating of any we’ve mentioned.

As for the types of rooms, you can choose between:

• 30 Water Cottages: Each with its own terrace overlooking the sea.
• 20 Loft Water Cottages: These are two-story cottages with the bed upstairs. They accommodate 4 people and, best of all, have stairs leading directly into the sea. That said, even though they are pricier, we think the decor of the standard water cottages is actually nicer.

Since this area is less well known than El Nido, these overwater villas offer even more privacy and exclusivity. If you combine this with a stay in El Nido—whether in another beautiful resort or somewhere more modest—you’ll get a more complete picture of what Palawan has to offer.

Book your overwater cottage at El Nido Resorts Apulit Island via this link

$$$ El Nido Resorts Lagen Island

The last of the El Nido Resorts hotels we’re covering is Lagen Island, which also features some of the most beautiful overwater villas in the Philippines. It sits on the island of the same name, south of Bacuit Bay, and is famous for its lush forest sanctuary. Because of this, it’s not unusual to spot colorful birds and monkeys right on the property.

Just like at Miniloc Island, the room rate includes most of the activities offered by the hotel, the most important being the island-hopping tours. While the location isn’t quite as spectacular as Miniloc’s, you won’t feel like you’re missing out for a second.

The resort has 51 rooms made from recycled wood, all with sliding glass doors that open onto private terraces.

• 18 Water Cottages: Built right over the sea, these beautiful, spacious cottages come with oversized sofas that are perfect for enjoying the views.
• 9 Beachfront Cottages: While they aren’t over the water like the water cottages, the views are just as wonderful—if not better—since you’ll be facing the sunset.
• 4 Forest Suites: A 70-square-meter room with views of the resort’s lush vegetation and the pool. The bathroom includes a luxurious bathtub in addition to the shower.
• 20 Forest Rooms: Very similar to the suites but slightly smaller.

Naturally, the hotel also has a bar, restaurant, gym, dive center, and a huge pool. In our opinion, the setting might be slightly less spectacular than Miniloc’s, though the rooms are definitely more spacious, and it also feels more family-oriented. Even so, we’re sure the experience will win you over.

Check prices and availability for El Nido Resorts Lagen Island here

$$$ Huma Island Resort and Spa

If you’re skipping El Nido on this trip and thinking of going to Coron instead, don’t worry—you’ll find some of the best overwater bungalows in the Philippines here, too. We’re talking about Huma Island Resort and Spa, located on Huma Island, a small island southwest of Busuanga.

The photos speak for themselves, but if you’re having trouble deciding, here are the types of rooms available:

• Water Villas: Exactly what you were looking for—64 overwater bungalows with their own jacuzzi.
• Beach Villas: Located right next to a beautiful beach, so they also boast sea views.
• Family Suites: A house with two adjoining rooms—perfect if you’re traveling with kids.
• Presidential Suite: A unit that combines 2 villas, with a huge living room, a sea-view terrace, and a pool.

In addition to these gorgeous overwater villas, the resort features 8 restaurants, a spa, a yoga pavilion, a hammam, a dive center, a library, a fitness room, a kids’ club, and an infinity pool. Of course, there are endless opportunities to enjoy the beach and nearby reefs, as well as kayaking, climbing, and excursions to beautiful nearby islands like Pass Island, Calumbuyan Island, and Black Island.

In 2021, it was renovated and changed ownership. We’ll have to wait and see how everything turns out, but it already looks promising.

Take a look at these overwater bungalows on Agoda

$$ Paolyn Floating House

How would you like to sleep right on a lagoon on Coron Island itself? These overwater bungalows are located specifically in Laknisan Lagoon, just a few meters from the popular Twin Lagoon—one of the must-see stops on the Coron island hopping tours. As the name suggests, they really are floating houses in the lagoon. That means there’s no reception lobby or typical pool area; instead, it’s a group of structures floating on the water, providing views that are simply mind-blowing. You can admire the impressive limestone cliffs and crystal-clear waters of this corner of the Calamianes without even getting out of bed.

You might be wondering if this is sustainable. The truth is, it’s genuinely eco-friendly. The houses are powered by solar panels, and neither the bathrooms nor the kitchen discharge anything into the sea; instead, waste goes into tanks and septic systems connected to service boats that transport it to other islands for proper disposal.

Originally, the name Paolyn Floating House referred to the first houseboat they built there, but they’ve gradually expanded to meet growing demand for this highly sought-after place to stay. Now, you can choose between:

• Paolyn Houseboat: 3 double rooms with bathrooms, 2 of them with a balcony. No air conditioning.
• Bamboo Houseboat: 4 double rooms with bathrooms and their own balcony, plus a sunbathing area. It has air conditioning, but if you want to use it, there’s an extra charge of 2,500 pesos per night.
• Glass Houseboat: A complete house with one double bedroom, living room, 2 bathrooms, and a “patio” with loungers and umbrellas.
• Mini Houseboat: 4 small double rooms with bathrooms and an 18 m² patio.

Whichever one you choose, you can eat at the restaurant—though it is a bit pricey—use the kayaks, paddleboards, and snorkeling gear (there are wonderful reefs nearby) for free, or sign up for one of the tours they offer on speedboats. Oh, and believe it or not, they even have Wi-Fi!

The amenities at these overwater bungalows might not be the most up-to-date, as they use local materials (mainly bamboo) to adapt to the stunning environment, but we guarantee it will be an experience you’ll never forget.

️If you’re looking for something cheaper, even if it’s not quite as unique, take a look at our article Best hotels to stay in Coron.

Book your overwater house in Coron here

$$$ Pearl Farm Beach Resort

Now let’s head south to another resort with overwater villas in the Philippines that’s sure to steal your heart. Pearl Farm Beach Resort is located on Samal, a small island just a few kilometers from Davao City, one of the country’s major cities, and known for its golden-sand beaches. The transfer from Davao Marina is included and only takes 30–40 minutes. Add to that the fact that the city has an international airport, and this becomes one of the easiest places on our list to reach.

Beyond its beautiful location, what really sets this hotel apart is its stunning design. They’ve managed to combine avant-garde elegance in the furnishings with the traditional textiles of the tribes of the southern Philippines. Add 5-star service, two pools, a kids’ club, several shops selling local handicrafts, a bar, a spa, and a restaurant serving international cuisine alongside local delicacies, and you’ve got a truly special place to stay.

As for the types of rooms:

• Samal House: Built over the water and inspired by the traditional stilt houses of the Samal tribes.
• Samal Suite: Similar to the Samal House, but a much larger two-story house. These aren’t directly over the sea, but they do sit on a platform with stairs leading straight into the water.
• Mandaya House: A unit made up of two bungalows, each with a double bed, private garden, balcony, and game room.
• Hilltop Room: A double room with sea and garden views.
• Malipano Villas: Located on a nearby island that Pearl Farm guests can visit for free. These villas are also built over the water and are so exclusive they even come with a butler.

All are wonderful, but if you want something truly special, we’d suggest going for the Malipano Villas.

Check out the rooms at Pearl Farm Resort at this link

$ Club Tara Resort

If you’re looking for overwater bungalows in the Philippines but don’t want to break the bank just to spend a night or two in one, you’ve come to the right place. Sure, you won’t get the high-end amenities offered by the previous resorts, but there’s no doubt this is one of the most Instagrammable spots in the country.

Located on the little-known island of Bucas Grande, Club Tara features wooden overwater cottages set in a crystal-clear lagoon. You can get here with the help of the resort, which organizes transfers from both Surigao Airport and Siargao. If you want to save some money, you can try arranging a transfer directly with a boatman in Siargao, which is a couple of hours away.

This 3-star resort offers a good range of room types:

• Overwater Cottage
• Family Room with Sea View (6 people)
• Mixed Dormitory Room (17 people)
• Family Room with Garden View (8 people)
• Standard Double Room with Garden View

All rooms have air conditioning, but without a doubt, we’d recommend choosing the first option, which can accommodate 2 adults and 1 child. These are the best-appointed—the others are quite basic—and come with a fridge, a balcony, and a jacuzzi with sweeping views of the lagoon.

The hotel is in a breathtaking, remote setting—possibly the most spectacular location of any on this list. You’ll have access to a restaurant, pool, bar, and massage service, but the real highlight is everything you can do around here. Kayaking, paddleboarding, snorkeling, walking to a nearby beach, and, of course, trips to Sohoton Cove (which we cover in our Siargao Island Hopping guide) are the big draws here—besides staying in an overwater bungalow for a bargain price.

Breakfast is included in the room rate. For other meals, you’ll have to use the restaurant, which is a bit basic and, frankly, quite pricey.

If it all sounds so good, why is the rating only 7.5? The truth is, although the resort has massive potential, it is far from being a luxury hotel. Unfortunately, the rooms could use a little TLC, and the staff could do with a bit more training. Even so, if you go in with realistic expectations and compare it to the price, we’re sure you’ll leave more than happy.

️ By the way, if you’re planning to combine your stay in these overwater bungalows with a visit to beautiful Siargao, don’t miss our article on the Best Resorts in Siargao and treat yourself.

Book your overwater bungalow at Club Tara Resort here

Other incredible resorts with sea-view rooms

As you can see, you won’t be short of options for finding the overwater villa in the Philippines you’ve been dreaming of. If, for whatever reason, none of these quite win you over, you can broaden your search and look at beautiful resorts that don’t necessarily have villas set right over the water. Here are some suggestions for amazing beach resorts with ocean-facing rooms that you’ll love:

• Amanpulo (Amanpulo Island)
• Qi Palawan (Palawan)
• El Nido Resorts Pangulasian Island (Pangulasian Island)
• Nay Palad Hideaway (Siargao)

️You can find many more in our article on the Best Resorts in the Philippines.

Where to book your overwater villa in the Philippines

Have you made your choice? Then it’s time to secure that reservation. Two booking platforms are especially useful in the Philippines: Booking and Agoda.

We prefer Booking because it’s more user-friendly, and we know from firsthand experience that its customer support is excellent if anything comes up. Even so, we recommend checking the dates for your overwater villa on both sites to see which offers the best price.

If you feel more comfortable being able to modify or cancel your reservation—perhaps because you prefer to play it by ear—the good news is that both Booking and Agoda usually offer free cancellation. Typically, this must be done at least 48 hours before arrival, but pay close attention to the fine print, as this depends entirely on the specific hotel.

As for how far in advance to book, it’s crucial that you reserve at least one or two months before your trip. This is essential if you plan to travel during Easter, Christmas, or Chinese New Year. Although these are exclusive accommodations, since there are only a handful of rooms like these, they can sell out fast.

Booking.com

Map of resorts with overwater bungalows in the Philippines

Below, you can check the map showing the locations of all the overwater bungalows in the Philippines we’ve mentioned. That way, you can easily work them into your Philippines travel route.

Frequently asked questions

Which resorts have overwater villas in the Philippines?
All the ones we’ve discussed in this article: El Nido Resorts Miniloc Island, El Nido Resorts Apulit Island, El Nido Resorts Lagen Island, Huma Island Resort and Spa, Paolyn Floating House, Sunlight Eco Tourism Island Resort, Pearl Farm Beach Resort, and Club Tara Resort. The area with the most options is El Nido, which is home to some of the country’s most prestigious resorts. If we had to choose, we would opt for El Nido Resorts Miniloc Island.

What are the cheapest overwater bungalows in the Philippines?
Staying in an overwater bungalow in the Philippines isn’t particularly cheap… If you want a similar experience without the luxury price tag, Club Tara Resort is an alternative. It’s located on Socorro Island and can be a great option if you’re planning to visit Siargao too.

How do I book my overwater bungalow in the Philippines?

The best way to do it is online and well in advance. The booking platforms that tend to work best in the Philippines are Booking and Agoda.

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We hope this roundup of overwater bungalows in the Philippines has inspired you. If you have any questions or suggestions, we’d love to hear from you in the comments. Remember, if you’re looking for accommodation, you’ll find suggestions in each of our destination guides, as well as in articles like Best Resorts in the Philippines and Hotels in the Philippines.