Indonesia: Coastal Cruises with Aqua Expeditions
With vast seas studded with islands of unique character, Indonesia is the perfect setting for a small ship cruising expedition.
Straddling three time zones and two mighty oceans, the country of Indonesia is the largest archipelagic country in the world. With open sea making up three-quarters of the country’s area, and 18,000 tropical islands stretching over 3,100 miles (5,000 km) longitudinally from East to West and 1,050 miles (1,700 km) latitudinally from North to South, Indonesia is a prime location in Southeast Asia for cruise adventures.
With its immense size, Indonesia also boasts astounding cultural diversity, with 1,300 ethnic groups and 652 documented languages, of which 11 have disappeared and 19 on the verge of becoming extinct. Year-round, a vast number of festivals are celebrated across the country, from ancient war rituals to folkloric traditions unique to each region or community.
Beyond the Southeast Asian country’s characteristic volcanic landscapes and colorful endemic wildlife, a cultural treasure trove of age-old traditions and well-preserved colonial-era relics await your discovery. Set sail through Indonesia on Aqua Blu, a luxurious vessel that enables you to enjoy the most rewarding coastal cruise itineraries in the world.
Discover our Itineraries
Here’s a look at some of the finest Indonesia small ship cruises to sail during your visit.
Located in the Coral Triangle between the major landmasses of Sumbawa to the west and Flores to the east, the waters of Komodo National Park are embraced by fast flowing currents from the Indian Ocean and warm tropical Indonesia seas enriched with volcanic nutrients. The result is a vibrant marine environment home to more than 1,000 species of marine life, including the manta ray, sea turtles and whale sharks, as well as over 260 species of corals. From shore to shore, the sheer diversity of sea life and different underwater environments make this region endlessly rewarding for both divers and non-divers alike.
Cruise Indonesia: Into Ocean Paradise
Coral Triangle: Known to be the global center of marine biodiversity, this region hosts over 6,000 species of fish and 76 percent of the world’s coral species. Over a 100 million people are dependent on this region for their sustenance. This is one of the foremost sites in the world for underwater exploration.
Komodo National Park spans across three major islands including Rinca, Padar, and the namesake Komodo Island. Along with this, there are numerous remote islands with a total surface area (marina and land) of 1817 square kilometers. The park provides refuge to thousands of marine and terrestrial species including whales, sharks, manta rays, and komodo dragons.
Complemented by a dry and sunny savannah-like tropical climate, Komodo National Park’s variety of land and sea experiences makes cruising an ideal way to discover the region. Built to set a new standard for luxury cruise ships, the speed, stability, and long-range capabilities of the Aqua’s small ship expedition guarantees five-star comfort, utmost exclusivity and an unrivaled immersion into the Park’s natural wonders. Access otherwise hard-to-reach marine sites and trekking routes where nature and wildlife flourish, often without other boats or humans in sight.
The islands of Komodo National Park
Known for its larger-than-life views and green-capped hills, Padar Island is one of the most picturesque places in Komodo National Park. The island brings together a unique landscape of crescent-shaped beaches with black and white sands.
Rinca Island is home to the famous Komodo dragons, the largest lizards in the world which are indigenous to this Indonesia archipelago. Rinca is also an ideal spot to snorkel alongside tropical fish and rays.
An official UNESCO World Heritage Site, a visit to Komodo Island is a quintessential part of an Indonesia cruise. The island features the volcanic hills and savannah, and is surrounded by clear turquoise waters. There are thousands of species of fish which live here, and visitors can spend hours snorkeling to find new sights.
Known for their volcanoes and palm-lined beaches, the Banda Islands are a group of islands in the north-east of Indonesia, commonly referred to as the Spice Islands. The islands have a rich colonial history, the remnants of which make them an exceptionally interesting destination to visit. For European settlers, the Spice Islands were appealing thanks to the presence of nutmeg, a spice that was worth more than its weight in gold.
The Spice Islands were the holy grail for famous old world explorers including Christopher Columbus and Ferdinand Magellan, who sought but never managed to find them. Eventually, the Spice Islands were discovered and the Dutch established and exercised control over them — with a monopoly on the nutmeg trade — from 1607 up until the late 18th century. In that time, the Dutch built up numerous colonial-styled architecture and extensive fortifications. Surrounded by the local town and the oldest nutmeg plantations on Earth, these structures remain mostly well-preserved.
Discover the Secrets of Spice
A Private Journey Across The Spice Islands: Among the most inspiring Indonesia cruises, a charter aboard the Aqua Blu is the perfect way to discover the Spice Islands. With expert naturalist guides who know the region like the back of their hand, you’ll be made privy to the secrets of Banda and the Maluku region.
The Spice Islands consist of a cluster of seven major islands, including the populated Banda Neira, Banda Besar and Pulau Run. Such was the significance of a monopoly of the Spice Islands, the Dutch East India Company, also known as the VOC, had traded Manhattan (in today’s New York City) for Pulau Run (an island just over a square mile in area) with the British in 1667.
Cruise Indonesia: Sail the Spice Islands
Known for its colonial relics, Banda Neira hosts iconic forts dating back to the 17th century. Among the most awe-inspiring is Fort Belgica, which features medieval towers at each vertex. Climbing up the towers is a rewarding experience, offering stunning views of the surrounding sea, Banda Neira town, and the Gunung Banda Api volcano.
Defined by its heritage, the island of Run was renowned in the 17th century for its production of nutmeg — a commodity that was worth more than gold at the time. In 1677, English colonizers gave up control of the island to the Dutch in exchange for the island of Manhattan, which is present day New York.
One of the uninhabited gems which is often overlooked while cruising Indonesia. While aboard Aqua Blu, enjoy a sunrise breakfast with Pulau Manuk’s 300-meter tall cliffs in the backdrop. The island is best known for its namesake volcano which rises three kilometers from the sea floor.
The name ‘Raja Ampat’ translates to ‘Four Kings’ in English. It is derived from local mythology which tells a story of a woman finding seven eggs, four of which hatched into boys. They grew up to become the kings of Raja Ampat’s four biggest islands: Salawate, Batanta, Misool, and Waigeo.
Raja Ampat captivates with the enigmatic beauty of its limestone karst island clusters bewilders explorers with dramatic landscapes that shelter secret lagoons, bays and beaches. In between excursions visiting the world’s most biodiverse environments, Raja Ampat offers the chance to find that one perfect private hideaway out of thousands. To put it simply, every day is a National Geographic moment right before your eyes.
Below The Sea
Diving in Raja Ampat: As one of the foremost marine hotspots on the planet, Raja Ampat is known for having over 200 internationally acclaimed scuba diving sites. It is one of the most popular destinations for an Indonesia cruise, hosting 600+ species of coral and more than 1,500 species of reef fish.
At almost every turn, the mesmerizing turquoise and blue hues of Raja Ampat’s waters constantly jostle for your attention and beckon you to swim and dive into the depths. Located at the heart of the Coral Triangle, the region is known to house every kind of underwater habitat imaginable; pristine reef flats, secret bays, swift channels, deep drop-offs, shallow seamounts, mangroves, marine lakes, and protected coral gardens are just a sample of the types of marine habitats that can be found in the roughly 20,000 square mile region.
Raja Ampat also happens to be in the middle of a major cetacean migration route and aggregation site where various whales and dolphin species have been sighted. This region is also the meeting point of the Indian and the Pacific Ocean, where a six-inch (15cm) average height difference between these two oceans creates an immense exchange of water carrying millions of aquatic eggs and larvae that spawn to life or serve as a vital source of food for marine animals.
Only in Raja Ampat
Cruising Indonesia and discovering the karst limestone islets and lagoons of Wayag is truly the adventure of a lifetime. In the West Papua region, the island features topography reminiscent of Norwegian mountains, except they’re dressed in tropical fauna instead of ice and snow. Located just south of the equator, sailing Wayag feels like a trip to the edge of the world.
Located in the West Papua province of Eastern Indonesia, Waigeo is the largest island in the Raja Ampat archipelago. The island hosts a lush tropical rainforest, within which flows the mystical Kali Biru river. This is one of only two places on Earth where it’s possible to spot the red bird-of-paradise.
A diving experience in the Raja Ampat isn’t complete without visiting Cape Kri. Located along the southern coast of Kri Island, this dive site is made up of large walls and slopes which are always teeming with marine life. Cape Kri holds the record for the most species spotted in a single 90-minute dive.
At the same time, the cooler water from deep-sea trenches and basins has also played a part in Raja Ampat’s stunning biodiversity. These environments offered wildlife shelter from glacial water in the ice ages, and today offers natural protection against rising sea temperatures that have resulted in the bleaching of other relatively unprotected coral habitats including the Great Barrier Reef and the Maldives. Endowed with natural geological defenses, Raja Ampat is truly Mother Nature’s last frontier.
Apart from its regular itineraries, Aqua Blu also offers highly exclusive cross-destination Indonesia cruises four times a year. Each of these sailings lasts 12 nights, exploring multiple destinations across East Indonesia in a single expedition. This is the perfect opportunity for those looking to discover the hidden gems of this region, which not many get a chance to see.
Every March, Aqua Blu sails from Raja Ampat to the Spice Islands – bringing together both itineraries for one unforgettable experience. This sailing combines the diving and marine-life-centric experiences – which Raja Ampat is best known for – with the rich local culture and heritage that can be found in the Spice Islands.
Immediately after, the expedition ship charts course for Flores for its next 12-night itinerary, combining another set of adventures in the Spice Islands with visits to remote and rarely visited places such as Alor, Damar, and Romang. After a season of sailing in Bali & Komodo National Park, Aqua Blu repeats this itinerary in reverse – sailing back to the Spice Islands at the end of September.
The final of the 12-night itineraries involves a trip from Spice Island to Raja Ampat every December.
Limited repositioning cruises
Aqua Blu’s cross-destination cruises offer a number one-of-a-kind excursions which can’t be found on any of the individual itineraries. As far as Indonesia cruises go, a 12-night sailing offers the best trip that can be had.
Asmat and West Papua are among the most uncharted destinations in all of Indonesia, rarely visited on board New Guinea cruises. Aqua Expeditions’ exclusive sailings in November 2025 will explore this region with stops at destinations including Momon, Cape Papisol, Triton Bay, and the jungles of Asmat.
Nestled along the western coast of New Guinea, the Asmat region is a land of mystique and wonder. It is home to one of Indonesia’s most enigmatic indigenous communities, the Asmat tribe. For centuries, this tribe has preserved its ancient traditions, with a strong focus on ancestor worship and rituals to maintain the balance of the natural world.
As guests embark on this extraordinary voyage aboard Aqua Blu, they will have the privilege of exploring the secrets of Asmat firsthand. Our itinerary includes visits to local villages steeped in rich heritage and culture, offering a rare opportunity to connect with the Asmat people and gain insights into their way of life.
West Papua & New Guinea Cruises
Secure a cabin on Aqua Expeditions’ highly limited sailings to the uncharted region of West Papua and New Guinea in November 2025. Featuring two 7N itineraries and two one-off cross-destination sailings exploring Spice Islands and Raja Ampat as well, plan the perfect all-inclusive adventure with snorkeling and diving excursions in the world’s most biodiverse waters.
Momon’s spectacular Kiti-Kiti waterfall is a jewel waiting to be discovered in the Nusalasi Bay Coastal Park Conservation Area of West Papua. The waterfall stems from a large river that originates in the highlands of the Papuan jungle. As it moves downstream, the river becomes a breathtaking natural waterfall that plunges a torrent of aqua blue directly into the ocean from the soaring emerald mountains above.
Over on Cape Papisol, guests can embark on a stunning up-river hike, starting from the island’s magnificent white-sand beaches and winding through lush, verdant forest for a stunning panoramic view of the Bomberai Peninsula, also known as the Bird’s Beak Peninsula for its distinct avian shape. This ecologically rich area is home to over 300 bird species, tree kangaroos, birds of paradise, and the endangered leatherback turtle, which nests on the pristine beaches.
Finally, Triton Bay offers a once-in-a-lifetime opportunity to swim alongside whale sharks. These gentle giants of the sea are attracted to the schools of bait fish that are caught underneath bagans – traditional Indonesian fishing platforms. Local fisherman have developed a fascinating, symbiotic relationship with these curious marine animals – known for their friendly behavior. This region also features sublime, uncrowded dive sites, home to a wealth of rare, endemic marine life and reefs decorated with flourishing soft coral that are considered the best in the world.