Indonesia Snorkeling – Many Destinations, Abundant Sea Life

Indonesia snorkeling is easily some of the best in the world. Indonesia is located in the Coral Triangle, where you can find the world’s highest coral and reef fish diversity on Earth.

Diverse hard coral reef with many diverse fish - Indonesia snorkeling

All of that life translates to some mind-blowing snorkeling. Floating over dense colorful coral reefs teeming with fish, hanging out over manta ray cleaning stations, watching the sea turtles and sharks that inhabit these reefs, seeing the large schools of pelagic fish out past the reef drop-off, getting up close to the interesting small nudibranchs, seeing the colorful giant clams, it just goes on and on.

Manta Ray at a cleaning station in Misool Indonesia

Indonesia, located in Southeast Asia, is the largest island country in the world. There are over 17,000 islands spread out over more than 700,000 square miles (nearly 2 million square kilometers). The country spans both sides of the equator so is a tropical climate, except in some high elevations. There are 130 active volcanoes in Indonesia.

Nine of Indonesia’s national parks are largely marine parks, where the marine life is protected. Additionally, the country has about 200 (and growing) marine protected areas that are managed in various ways. These places can provide wonderful Indonesia snorkeling with abundant sea life that is not afraid of you.

School of fusiliers in blue water in Indonesia

In a number of areas of Indonesia, the amount and diversity of the sea life can be linked to an influx of fresh sea water flushing through the area with every tide. Sometimes there are upwellings of cool sea water from deep in the ocean. This moving water keeps these reefs healthy. Places where this is particularly evident are in Raja Ampat, Komodo, and Alor.

Indonesia Snorkeling – What Can You See?

Edge of a colorful coral reef drop-off with huge school of red anthias in Indonesia

Of course one of the highlights of Indonesia snorkeling is the incredible coral reefs. There are countless shallow reefs perfect for snorkeling. Many of the reefs are fringing around the islands, with plateaus you can explore. Then those reefs will often drop off quickly and there is always something interesting to see out in the dark blue water. There are vertical walls covered in coral that come right to the surface. There are sea mounts and pinnacles that reach the surface. And there are lagoons with sand and patch reefs, sea grass beds, and mangroves to explore.

As for corals, you can see nearly any kind you would like from a vast array of hard corals, like table and staghorn corals, to diverse soft corals, like leather corals, fans, and more.

The reefs are literally teeming with fish, in schools and individuals. Clouds of damselfish and anthias are everywhere. Gorgeous butterflyfish and angelfish are easy to spot. Massive schools of fusiliers streak by the reefs. If you are lucky you can recognize through their camouflage scorpionfish, frogfish, and crocodilefish. The colorful parrotfish and wrasses are a treat to see. Anemones of all colors are homes to the variety of clownfish you can watch here. The sweetlips, Mandarinfish and gorgeous lionfish will make your trip!

Many areas of Indonesia are known to be manta ray cleaning stations, so chances are high you can snorkel with the incredible giants. Particularly in areas where they are protected, sharks are regulars on the reef and a joy to see. If you snorkel at night you might get to watch the walking or epaulette sharks that are only found in the Coral Triangle and Australia. Out in the deep blue water you could see a Mola mola, whale sharks, eagle rays and more. And some of the best creatures to spot are in the same family, octopus, squid, and the amazing cuttlefish.

Anemone and clownfish in Indonesia

Indonesia Snorkeling – Where to Go?

We have personally been and recommend the Indonesia snorkeling places below.

Spots We’ve Been Snorkeling in Indonesia

Raja Ampat

Raja Ampat is probably the most well-known area for snorkeling in Indonesia. The Coral Triangle is the most bio-diverse marine environment in the world, and Raja Ampat has the most species of marine life in all of the Coral Triangle. The snorkeling here can be separated into two general geographical areas, north and south. We have snorkeled both. Northern Raja Ampat snorkeling is exceptional. You can read all about it and see lots of pictures here. Read about southern Raja Ampat in our next section, Misool.

Cuttlefish over staghorn coral in Raja Ampat


Misool, the southern region of Raja Ampat, has astounding Indonesia snorkeling! There is a large marine protected area and that protection shows in the sheer number and diversity of sea life. Misool boasts massive numbers of fish and coral species, not to mention manta ray cleaning stations and sharks galore. Read all about our snorkeling experience in Misool here.

Black-tip Reef Shark with remora in Misool Indonesia


Alor, in East Nusa Tenggara province, has some of the healthiest reefs we have ever seen, and they are teeming with fish life. We even got to swim with a huge Mola mola! It is not a place that has been discovered by tourism and is a joy to visit. The currents and upwellings in the area are responsible for these healthy reefs, but require a knowledgeable guide for safe snorkeling. Read all about our experience snorkeling Alor here.

Soft and hard corals with tons of fish on an Alor Indonesia reef
Mottled green giant clam in coral reef in Indonesia

Komodo National Park

We loved the Indonesia snorkeling we found in Komodo National Park. This park offers protections for the marine life and many of the reefs are wonderful for snorkeling. There are places to see huge sea turtles here and some manta ray cleaning stations to swim with these incredible creatures. This park is accessible by boat for snorkeling. Read all about how we snorkeled Komodo here.

Wakatobi National Park

We were lucky enough to snorkel some of the reefs in the famous Wakatobi National Park. These Indonesia snorkeling reefs have a diverse variety of hard and soft corals, and a great variety and number of colorful reef fish. Wakatobi is a region southeast of Sulawesi named for the four main islands in the area. The first letters in the names of those four islands, Wangi-wangi, Kaledupa, Tomia, and Binongko, make the portmanteau word Wakatobi. Read all about snorkeling Wakatobi and how to do it yourself here.

Wakatobi reef with leather corals and a mix of fish

Bunaken National Park

We snorkeled Bunaken National Park on the same trip as Wakatobi. It is in North Sulawesi and some islands a little ways offshore of the city of Manado. Snorkeling there was a treat with its lively fringing reefs and walls full of sea turtles. It is probably the most easily accessed Indonesia snorkeling destination we have visited so far. There are also many accommodation options in the park and can be quite affordable. See our pictures, video and Bunaken snorkeling information here.

Clownfish in large anemone is Bunaken


We snorkeled the islands of Halmahera as part of an Indonesia liveaboard snorkeling trip. Halmahera is an island group between Raja Ampat and Sulawesi in northern Indonesia. This area is just starting to be explored in detail and many of the snorkel sites have yet to even be named.

The reefs there were simply teeming with damselfish and anthias. The hard and soft corals were diverse and healthy. The reefs were shallow and wonderful for snorkeling. Read all about what the snorkeling is like in Halmahera.

Dendronephthya and staghorn corals with damselfish on Halmahera reef

Lembeh Strait

We were lucky enough to be able to snorkel this unique place as part of a liveaboard trip that visited three areas of Indonesia. Lembeh Strait is known for muck snorkeling, seeing rare critters that live in areas of black sand. That was fun and we were also surprised by the healthy reefs and amazing wall we got to snorkel there, too. Read all about our experience snorkeling Lembeh Strait here.

Ochre-striped Cardinalfish with staghorn coral in Lembeh Strait

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More Indonesia Snorkeling Places

Cenderawasih Bay National Park

The largest marine national park in Indonesia, this is a very remote destination. Well-known for the year round whale shark population that is easy to snorkel with, it is primarily visited by liveaboard diving boats. Our trips partner is offering a Cenderawasih liveaboard snorkeling trip if you want to get to this wonderful destination.

School of Panda Butterflyfish in Indonesia
Snorkelers over branching coral and damselfish in Misool Indonesia

Kalimantan (Borneo)

Kalimantan is the part of the large island of Borneo that belongs to Indonesia. There are some smaller islands with healthy coral reef and lots of sea life offshore northeast of Kalimantan.

Bali and the Three Gilis off Lombok

These are probably the most popular places for Indonesia snorkeling. Bali is an easy island to reach and welcoming to visitors. The best snorkeling is reportedly on the east side of the island, in and near Amed, but there is also some on a small neighboring island in the northwest called Pulau Menjangan. In Amed you can enter from the beach for many snorkeling spots. Pulau Menjangan is reached by boat tour.

The Gilis are three well-known small islands east of Bali off the coast of the larger Lombok. Gili Trawangan, Gili Meno, and Gili Air are popular and busy, but have shore snorkeling around them, so you don’t need to get on a boat.

Best Time of Year for Indonesia Snorkeling?

Most regions of Indonesia have their own weather patterns, so you need to look into the area you are considering specifically. Generally Indonesia has a dry season between May and October and a wet season between November and April. As winds are most important for snorkeling conditions, they are generally predictable and moderate. There are monsoons and they generally blow in from the south and east June through October and from the northwest November through March.

Getting There?

For your Indonesia snorkeling trip, you will mostly likely fly into either Bali or Jakarta if you are arriving from distant countries. From there you can fly to all other areas of Indonesia on one of the domestic airlines. Here are a few destination airports: for Raja Ampat, you will fly into Sorong; for Komodo you will fly into Labuan Bajo; for Bunaken you will fly into Manado on Sulawesi. The Gili islands can be reached from Bali by ferry.

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