Five island-hopping routes in Indonesia, from an easy Bali-to-Nusa day boat to a Raja Ampat expedition. How each works, crossing times, best season, and how to plan.
By Asik Travel Editorial7/13/20269 min readIndonesia is not one destination. It is more than seventeen thousand islands strung across three time zones, and the single best way to feel that scale is to travel between them by boat. Island hopping here can mean a thirty-minute skip from a Bali beach to a cliff-backed cove, or it can mean a week of ferries and longboats to reach reefs almost nobody dives. Both count, and the trick is matching the route to the kind of trip you actually want.
We run trips across these islands, so this guide is built the way we plan them: as a ladder. It starts with the easy, do-it-in-flip-flops hops close to Bali and climbs, route by route, toward the remote expeditions that take real commitment. Read down until the effort stops sounding fun, and that is roughly your route. Each one links through to the full guide if you want the fine detail.
Three things decide which route fits you: how much time you have, how far off the grid you are happy to go, and what you want to see when you get there. A long weekend keeps you near Bali. A week opens up Komodo or the far Sulawesi islands. Two weeks and a tolerance for long boat days puts Raja Ampat in reach. As a rule in Indonesia, the reward scales with the effort: the reefs get healthier, the beaches emptier, and the prices for a boat go up as the crowds thin out.
| Route | Difficulty | Time you need | Getting between islands |
|---|---|---|---|
| Bali to the Nusa Islands | Easy | A day to 3 days | Fast boats, 30 to 45 minutes |
| Lombok and the Gili Islands | Easy to moderate | 3 to 5 days | Fast boats and cheap public boats |
| Flores and Komodo | Moderate | 3 to 5 days | Day boats or 2 to 3 day sharing trips |
| The Togean Islands | Hard | A week or more | Long ferries, then resort boats |
| Raja Ampat | Expedition | 8 days or more | Sorong ferry, then homestay or liveaboard boats |
The gentlest island hop in the country runs from Bali across a narrow strait to the three Nusa islands: Penida, Lembongan, and Ceningan. Fast boats leave all day from the consolidated Sanur port, more than ninety departures on a normal day, and cross to Nusa Penida or Lembongan in roughly thirty to forty-five minutes for about 150,000 to 250,000 rupiah one way, which is around 10 to 20 dollars. You can leave a Bali breakfast behind and be snorkeling off a new island before lunch. This is island hopping with training wheels, and it is the one most first-timers start with.
Nusa Penida is the dramatic one, all sheer cliffs and the postcard viewpoint at Kelingking Beach, plus manta rays you can snorkel with year round at Manta Point. Lembongan and Ceningan next door are smaller and mellower, joined by a yellow suspension bridge you can walk or scooter across. You can do Penida as a long day trip from Bali, but staying a night or two lets you catch the viewpoints before the day-trip boats arrive and turns a rushed checklist into an actual island break.
Go early to beat the day-trip crowd
The Nusa viewpoints and Manta Point get busy from mid-morning when the day boats land. If you stay overnight on Penida or Lembongan, hire a scooter or driver for first light and you will have Kelingking and the manta cleaning stations to yourself for an hour before the crowd arrives. It is the single biggest upgrade to the trip.
One island east of Bali sits Lombok, and off its northwest coast float the three Gili islands, car-free specks of white sand and turquoise water. You can reach the Gilis two ways, and the price gap between them is startling. Tourist fast boats run direct from Bali in around one and a half to two and a half hours for roughly 35 to 70 dollars, which is simple but pricey. Or you make your own way to Lombok and take the local public boat from Bangsal harbour for about 20,000 rupiah, near a dollar and a half. Same islands, thirty times the fare. Our guide to the Gili Islands breaks down which Gili suits which traveler: Trawangan for buzz, Air for balance, Meno for near-total quiet.
The Gilis are the obvious draw, but Lombok itself rewards anyone who lingers. It has the surf beaches of the south around Kuta, waterfalls in the hills, and the volcano Rinjani looming over all of it. Stitching the two together, a few days island-hopping the Gilis and a few on Lombok, makes one of the most satisfying beginner routes in the country. The full Lombok and Gili itinerary lays out how many days to give each, and how to move between them without wasting a morning at a harbour.
Fly to the fishing-town-turned-boat-hub of Labuan Bajo on Flores and you are at the gateway to Komodo National Park, which is island hopping at its most iconic: pink-sand beaches, the clifftop view from Padar, manta rays, and the dragons themselves. Here the hop is the whole point. You can do it as a day trip by speedboat or a two to three day sharing trip that sleeps aboard a wooden boat, and which you choose changes the trip completely. Shared overnight trips start around 220 dollars a person for two days and one night, rising with the comfort of the boat, and they include your meals, snorkeling gear, a guide, and the harbour fees. Day boats are cheaper and get you the headline stops; the overnight trips reach the quieter islands and catch the light when the day boats have gone home.
Komodo now caps daily visitors, so book ahead
From 2026, Komodo National Park limits how many people can enter each day, with a cap of around 1,000 visitors that takes full effect in the April high season. In practice that means peak-season boat trips sell out earlier than they used to. If you want Komodo in the dry season, lock in your dates and your boat well before you arrive rather than turning up and hoping for a spot.
Komodo has a park entry fee on top of the boat, and it is worth reading up on before you go so the cost does not surprise you. Beyond the park, Flores keeps going: a spectacular overland road runs east past traditional villages to the three-colored crater lakes of Kelimutu. If you have the days, pairing a Komodo boat trip with a stretch of Flores overland is one of the best weeks in Indonesia. Start with how many days to spend in Labuan Bajo to size the trip.
Now the ladder gets steeper. The Togean Islands sit in the middle of a calm gulf in Central Sulawesi, and reaching them takes a domestic flight plus a long overland leg plus a ferry, so this is not a casual add-on. What you get for the effort is the Indonesia of fifty years ago: stilt villages, a lake full of stingless jellyfish, and reefs so lightly visited the fish are not shy. Movement between the islands is by resort longboat, at the pace the sea allows. The full Togean Islands guide covers the routes in via Ampana or the overnight Gorontalo ferry.
This is slow hopping, and it only works if you lean into it. Plan a week minimum, carry all your cash because there are no ATMs, and hold a buffer day for the ferries, which run on weather rather than timetables. If the Togeans appeal but you want to understand how they sit among Sulawesi’s other islands, the Central Sulawesi itinerary and the Luwuk Banggai guide both pair naturally with them.
Build buffer days into every remote hop
The further east and off-grid you go, the more the boats answer to the weather instead of the clock. On the Togeans, in the Banggais, and across Raja Ampat, never plan to leave an island on the same day as an onward flight. Keep at least one spare day, ideally two, so a cancelled crossing costs you a lazy afternoon rather than a missed plane home.
At the far end of the country and the far end of this ladder is Raja Ampat, a scatter of islands off West Papua that holds the richest marine biodiversity on Earth. Getting here is a mission: a long flight to Sorong, then the two-hour ferry across to the main island of Waisai for about nine dollars, then a smaller boat out to your homestay or liveaboard. There are now two conservation fees, a marine park permit and a visitor ticket, together about a million rupiah or sixty-odd dollars per foreign visitor, and as of 2026 you can pay both online before you arrive instead of only in cash at Waisai. Read how to get to Raja Ampat before you go, because the connections do not forgive a tight schedule.
Once you are there, hopping happens two ways. Stay in the Papuan-run homestays and you move between islands by local longboat, simple and cheap and close to the community. Or book a liveaboard and the islands come to you, the boat repositioning overnight so you wake up at a new reef each morning. Either way this is the trip you build up to, not the one you start with. Our Raja Ampat travel guide covers homestays versus liveaboards, the permit, and the best time to go.
For every route on this list, the dry season is your friend. Roughly April to October brings the calmest seas, the clearest underwater visibility, and the most reliable boats, which matters more the further off-grid you travel. The wet season from November to March is not off-limits near Bali, where crossings are short, but for the Togeans and Raja Ampat it turns long open-water legs rough and gets the smaller boats cancelled. If your trip hinges on a boat, the dry months stack the odds in your favor.
You can piece any of these routes together yourself, and plenty of people happily do. The catch is the joins: the flights that have to line up with ferries that do not sell tickets online, the resort transfers that depend on the same boats, and the weather calls on whether a crossing is safe. That chain is the real work of island hopping in Indonesia, and it is exactly what we handle. If you would rather hand over the logistics and just show up for the good part, you can plan a trip with us, or browse our small-group and private trips to see the routes already built. Not sure which islands to start with? The best Indonesian islands for a first trip is the place to begin.
Written by
Asik Travel Editorial
Local travel editors
We write from the islands we sell, with first-hand notes from our guides and operators.
The easiest is Bali to the Nusa islands (Penida, Lembongan, Ceningan). Fast boats leave through the day from Sanur and cross in about 30 to 45 minutes, so you can hop across for a day trip or an easy overnight without any long travel. It is the route most first-timers start with.
Two ways. Tourist fast boats run direct from Bali (Padang Bai or Serangan) to the Gilis in roughly two hours, which is the simplest option. Cheaper is to cross to Lombok and take the local public boat from Bangsal harbour, which costs a fraction as much but takes more coordination. See our Gili Islands and Lombok-Gili itinerary guides for details.
The dry season, roughly April to October, is best across every route. It brings the calmest seas, the clearest water, and the most reliable boats. This matters most for remote routes like the Togean Islands and Raja Ampat, where the wet season (November to March) makes long open-water crossings rough and gets smaller boats cancelled.
For the easy Bali-area routes you can often book fast boats a day ahead or on the spot. For Komodo sharing trips, remote ferries, and Raja Ampat homestays or liveaboards, book well ahead: capacity is limited, tickets are frequently not sold online, and the connections have to line up. Building in a buffer day for weather is wise on any remote route.
Raja Ampat has the richest marine life on Earth and is the top choice for serious divers, though it takes the most effort to reach. For easier access, Komodo offers manta rays and dramatic reefs from Labuan Bajo, and Nusa Penida has year-round manta snorkeling a short boat ride from Bali. The Togean Islands reward those willing to travel far for quiet reefs.
It depends on the route. Bali to Nusa works as a day trip or a 2 to 3 day break. Lombok and the Gilis suit 3 to 5 days, as does Flores and Komodo. The Togean Islands need a week minimum because of the long journey in, and Raja Ampat is best with 8 days or more once you factor in the travel to reach it.
