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, across these 7,000+ islands you have the option to stay in overwater hotels in the Philippines that rival the famous spots in the Maldives or French Polynesia. Typically built with wood and featuring the country’s traditional thatched or nipa roofs, you usually won’t be lacking any modern comforts inside—in many cases, you’ll even have your own pool or jacuzzi with sweeping ocean views.

Important details about hotels with water 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 cabins in the Philippines are located around El Nido. In our opinion, this is the prime spot, as the landscapes you’ll see right from your cabin are spectacular. When you wake up, you’ll be greeted by towering black limestone cliffs merging with the 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, as almost all of them (if not all) include boat transfers from El Nido Airport, located at Lio Beach.

Likewise, since you’re in secluded spots and it isn’t feasible to pop out of the hotel every time you need to eat, many offer packages with full board or, at the very least, breakfast. Of course, they also have restaurants for à la carte dining. Adding to these conveniences are exclusive spas, the option to grab a kayak or paddleboard, and other activities. In the case of El Nido, almost all resorts include 1 or 2 island hopping tours in the room price, 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 want to hold a special ceremony or a full-blown wedding in the Philippines (which you can later legalize back home), you can also have it organized 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 easily view the overwater villas in the Philippines we’ve selected for you. We thought it was important to highlight the location, price, and the rating given by other travelers.

RESORTS WITH OVERWATER BUNGALOWS IN THE PHILIPPINES	AREA	RATING	PRICE/NIGHT
El Nido Resorts Miniloc Island	El Nido	8.9 – Fabulous	From €445
El Nido Resorts Apulit Island	El Nido	9.3 – Fantastic	From €360
El Nido Resorts Lagen Island	El Nido	8.9 – Fabulous	From €430
Huma Island Resort and Spa	Coron	7.4 – Good	From €550
Paolyn Floating House	Coron	9.5 – Exceptional	From €300
Pearl Farm Beach Resort	Siargao	8.7 – Fabulous	From €240
Club Tara Resort	Davao	7.5 – Very good	From €49

The best overwater bungalows in the Philippines

Let’s analyze these accommodations one by one. Check out the photos—you’re going to be amazed! You can surely 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 premier hotel groups in the Philippines, boasting several properties scattered around Palawan that are an absolute delight. The first one we’re highlighting is located on Miniloc Island, home to El Nido’s most famous lagoons: Small Lagoon and Big Lagoon. This guarantees a stunning setting and the chance to explore by kayak or paddleboard on your own before the crowds roll in. It is truly one of the best resorts in El Nido.

The service is worthy of a 5-star hotel, and to top it off, impressive island-hopping tours are included in the room price. 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 typical roof style, 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 your spot. 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 complex offering gorgeous panoramic views, these are two-story cottages for 4 people.
• 12 Beachfront Cottages: With capacity for 3 people, 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. In short, 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 of the hotels in the El Nido Resorts chain isn’t located strictly in El Nido, but it still delivers that overwater bungalow experience in the Philippines you’re looking for.

It’s located on Apulit Island, a private island in Taytay Bay—that is, on the coast of Palawan opposite El Nido and about 40–50 minutes from the mainland. Because of this, access is a bit more of a trek, and the standard El Nido island-hopping excursions aren’t offered here. That doesn’t mean there’s nothing to do—in fact, the snorkeling is epic and includes a sunken Japanese ship and a giant clam sanctuary. You can also climb imposing limestone cliffs, explore caves, and visit a beautiful spot called White Island that you’re bound to fall in love with. In fact, this resort has the highest rating of all the ones 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 guarantee privacy and exclusivity. If you combine this with a stay in El Nido—whether in another epic resort or more modest accommodation—you’ll get an even more complete picture of what Palawan is all about.

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

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

• 18 Water Cottages: Built right over the sea, these beautiful, spacious cottages feature epic sofas for enjoying the views.
• 9 Beachfront Cottages: While they aren’t over the water like the former, 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 (though the rooms are definitely more spacious), and it feels more family-oriented, but we are 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 don’t feel like going to El Nido on this trip but are thinking of swapping it for Coron, 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 slice of land 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 combining 2 villas with a huge living room, terrace with sea views, 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 underwent renovations and changed ownership. We’ll have to wait a bit to see the final changes, but it already looks promising.

Take a look at these overwater bungalows on Agoda

€€ Paolyn Floating House

How would you like to sleep right inside 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 are literally floating houses in the lagoon. That means there’s no reception lobby or typical pool area; instead, it’s a cluster of structures floating on the sea, providing views that are simply mind-blowing. You can gaze at the impressive limestone cliffs and crystal-clear waters of this corner of the Calamianes without ever leaving your bed.

You might be wondering if this is sustainable. The truth is, it’s totally 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, but they have gradually expanded to meet the growing demand for this highly sought-after accommodation. 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.

Whatever you choose, you can eat at the restaurant (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 modern, 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 Where to stay in Coron.

Book your overwater house in Coron here

€€€ Pearl Farm Beach Resort

We’re heading south to tell you about another resort with overwater villas in the Philippines that will 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) 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 most accessible spots on our list.

Beyond its beautiful location, what defines this hotel is its impeccable decor. They’ve managed to combine avant-garde elegance in the furnishings with the traditional textiles of the tribes of the southern Philippines. Add to this 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.

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 above, but a much larger two-story house. These aren’t literally hovering over the sea but sit on a platform with stairs providing direct access to the water.
• Mandaya House: A unit composed 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 suggest you opt 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 cash, you can negotiate a transfer with a boatman in Siargao, which is a couple of hours away.

This 3‑star resort offers rooms that vary quite a bit:

• 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. Without a doubt, we encourage you to choose the first option, which fits 2 adults and 1 child. These are the best decorated—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—perhaps the best location of all the ones in this article. You’ll have access to a restaurant, pool, bar, and massage service, but the real highlight is the activities around you. Kayaking, paddleboarding, snorkeling, walking to a nearby beach, and, of course, the excursion 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 everything sounds so good, why is the rating a 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 some extra training. Even so, if you go with managed expectations and compare it to the price, we’re sure you’ll leave more than happy.

️ By the way, if you are going 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 them win you over, you can broaden your search and focus on cool resorts that don’t necessarily have structures 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 work particularly well in the Philippines: Booking and Agoda.

We prefer the former because it’s more intuitive and we know firsthand that they have solid customer support 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 directly 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 very few rooms of this type, they can sell out fast.

Booking.com

Map of resorts with overwater bungalows in the Philippines

Here you can check the map for the locations of the overwater bungalows in the Philippines we’ve mentioned. This way, you can easily incorporate 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 boasts some of the most prestigious ones. 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 vibe without the luxury price tag, Club Tara Resort is an alternative. It is located on Socorro Island and can be a good add-on if you plan to visit Siargao.

How do I book my overwater bungalow in the Philippines?

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

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We hope we’ve whetted your appetite with these overwater bungalows in the Philippines. If you have any questions or suggestions, we’d love to read them in the comments. Remember that 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.