Imagine gliding through crystal-clear waters, discovering hidden sea caves, and diving into some of the bluest water you’ve ever seen. That’s exactly what you can expect on a boat trip in Malta.
I spent several weeks exploring these islands by land and boat, including around Valletta and the Three Cities, as well as private charters to my favorite spot– Comino Island’s Blue Lagoon. After a lot of exploring every swimming spot I could find—I’ve figured out which boat trips are truly worth your time (and which ones aren’t).
This guide is all about helping you experience the best of Malta from the water, just like I did.
1. Comino, Blue Lagoon & Gozo Full-Day Boat Cruise
This epic 2 Island Boat Cruise is a great option and the tour I ended up booking twice because it’s such a great mix of adventure and relaxation.
If it’s your first time in Malta, this is hands-down one of the best ways to experience both Gozo and Comino without feeling rushed, visiting all the top attractions on both Gozo and Comino including the Comino Caves, The Blue Lagoon, and highlights on Gozo like the Citadel in Victoria and Xlendi Bay!
Departing from the Buġibba, the boat cruise starts off with a tour of the most spectacular rocky cliffs, caves, and historical landmarks, such as St Paul’s Islands and Santa Maria caves. Make sure you have your camera ready for some incredible shots because this is one of the most picturesque places in the country!
Then, Captain Kevin takes passengers for a 1.5-hour stop in the crystal clear waters of Blue Lagoon, Comino. When I asked him about the best time to visit, he suggested aiming for a morning departure (around 9 am) to beat the midday rush. If you’re going in peak season, the Blue Lagoon gets crazy busy by noon, so my top tip is to head straight to the far-left side of the lagoon where the crowds thin out.
You can swim and snorkel, catch some rays on the upper deck, make a splash from the boat’s slide or simply take in the incredible surroundings.
The boat will then set sail to the island of Gozo, where you’ll have 3 hours dedicated to sightseeing. You can either book a shuttle bus on the day to take you to Victoria and Xlendi Bay or opt to do your own thing via public transport. (I recommend taking the local bus as it's cheap and easy).
As the boat cruise makes its way back to Malta, you’ll pass by more natural wonders such as the Crystal Lagoon, sea caves, and St Mary’s Tower.
Tip: I made the mistake of assuming Gozo’s bus system was as efficient as Malta’s—spoiler: it’s not. If you’re on a time crunch, definitely book the shuttle bus at the start of the tour. The last time I visited, I missed the return boat by 10 minutes because I relied on the public bus, which runs infrequently and sometimes doesn’t show up at all.
2. Lazy Pirate Boat Party
Fancy a night out with a difference? The Lazy Pirate Boat Party is one of the best boat trips you can book if you’re traveling with a large group of friends or if you’re a solo traveler who’s interested in mingling with new people.
The famous “Fernandez 2” departs Sliema Ferries at approximately 6:30 pm. Expect great tunes from the DJ, lots of dancing, spectacular views of the Mediterranean Sea, and an open bar jam-packed with spirits, beers, and soft drinks.
What’s more, you can also head to the afterparty in Paceville after the boat returns to Sliema at around midnight.
Needless to say, the Lazy Pirate Boat Party has all the right ingredients for a memorable night out if that's what you're looking for from a Maltese boat trip!
3. Marsamxett Harbour & Grand Harbour Cruise by Night
Beat the heat with one of the best boat tours that will take you around the spectacular Marxamxett & Grand Harbour night cruise.
This delightful guided harbor cruise will give you a taste of Malta’s rich history and culture as you sail into Marsamxett Harbour (on the Sliema Side) as well as the Grand Harbour (Valletta Waterfront and Three Cities).
Throughout this 90-minute tour, complete with an ongoing commentary, you’ll also get the chance to visit 10 creeks. This is a boat tour that is great for those who want to learn about the unique history of these harbours.
Experiencing the historic harbour by night was one of my favorite boat experiences in Malta. Seeing the city light up some of the most significant fortifications surrounding Malta’s capital, Valletta was something I'll never forget.
Before heading back to its departure point in Sliema, the boat tour ends with a visit to the Three Cities – Senglea, Cospicua, and Vittoriosa.
4. Private Boat Charters to Comino Blue Lagoon
Are you looking to book a more exclusive trip to Comino? As much as I enjoy group tours, a private boat charter reserved just for you and your group of traveling friends is arguably a much more freeing experience since you can choose an excursion that can be catered towards your tastes and preferences (without having to wait in queues).
I've had great experiences going on private boat trips with Outdoor Explorers. This is a local business run by two brothers and they showed us some secret caves we would have missed otherwise.
Whichever private boat tour you book, in Malta, you will have the option to book a private boat tour for half a day, a full day, or a sunset tour. Amongst the perks that come with a private boat trip to Comino, you’ll get to choose the pick-up point and the stops you’d like the skipper to make along the way.
Based on my experience, I highly recommend planning a route that will include stops at the Blue Lagoon and Crystal Lagoon as well as some of the most fascinating sea caves such as Popeye’s Cave, the Lovers Cave, and the Santa Marija Caves. However, make sure to plan with your skipper as they'll be able to show you some local sites as well.
You can swim, sunbathe on deck and use the snorkeling equipment that is almost always provided on board to explore hidden gems and marine life. What’s more, you can bring your own food on board or ask the skipper to make a couple of stops along the way.
And on that note, here are some of my favourite private charters that offer the best boat trips to Comino, Blue Lagoon.
Tip: One trick I learned: if you ask your skipper to take you past Il-Ħalfa Rock, you’ll get a secluded swim stop with zero crowds. Most boat tours don’t go here, but it’s easily one of the best snorkeling spots near Comino—especially if you’re looking for marine life like octopuses and parrotfish.
Outdoor Explorers Private Boat Charter to Comino
The private boat trip with Outdoor Explorers was one of my favorite highlights of my trip to Malta. Run by two local brothers, they offer flexible trips to ensure you get ample time on your hands to truly make the most of your day in Comino.
Jump in the clear waters, explore and snorkel all the hidden gems below the surface, catch some rays and so much more! I especially liked the flexibility they offered me to plan an island hopping itinerary and they offered to pick me up from my hotel which was very convenient.
4-hour Private Boat Trip & Comino Charter
If you're looking for a private boat tour that is easier on the wallet, this 4-hour private boat trip and charter on Viator is a great bet. This trip is run by Johnny, a local who is well known for his expertise and knowledge around the islands.
He offers pickup in Mgarr, Gozo or Cirkewwa and the 4-hour trip includes stops at the magnificent sights, sea caves and beaches around Comino including:
- Blue Lagoon
- San Niklaw Bay
- Santa Marija Bay
3-Hour Sunset Private Boat Trip
It's no secret, the best sunset spot in Malta is from a private boat on the water! And, with this sunset boat trip, you can have this experience, as long as you book ahead!
I recommend this tour for couples and small groups who’d like to explore the Maltese Islands during a quieter time of the day. Since this is a sunset private boat trip, expect glorious hues as the sun sets over the crystal clear waters of Comino and Gozo.
5. Ultimate Kayak Adventure
One of my favorite experiences in Malta was a guided kayaking adventure on the south coast.
This is one of the best boat trips that allows you to discover Malta’s hidden gems that are scattered along the south coast of Malta. Whether you’re a beginner or an experienced kayaker, you’ll be given some tips and tricks from the instructor before you head out but they will base the itinerary on your skill level.
To name a few, you’ll stop by scenic spots such as the Munxar Window and Hofriet Window. What’s more, you can also bring along your snorkelling gear to discover more treasures under the sea.
6. Blue Grotto and Marsaxlokk Half-Day Tour from Valletta
This half-day tour from Valletta takes you to two of my favourite places on the Southern Coast of Malta, the Blue Grotto, as well as the charming fishing village of Marsaxlokk.
After setting sail from Valletta, you’ll start off with a stop in Blue Grotto, where you’ll get to see the actual site as well as other nearby rock formations and sea caves. Meanwhile, Marsaxlokk is known for its traditional luzzu fishing boats as well as the famous Sunday market.
I think this is one of the best boat tours to take in Malta, especially if you’re pressed for time since you'll get to see two iconic spots in one day!
Tip: If you’re visiting the Blue Grotto, skip the midday boat tours and aim for an early morning or late afternoon slot. I've been a few times and by far the best light is at around 9 am or 5 pm– creating a stunning neon-blue effect inside the caves, which you won’t get at noon.
I hope this quick travel guide has helped you find an epic boat tour to book for your trip to the Maltese Islands! If you have any further suggestions, please let me know in the comments below!
- 70+ Things to do in Malta - my ultimate Maltese Travel Guide covering all the must-see attractions and hidden gems in the archipelago.
- 40 Amazing Things to do on Gozo - I explored every corner of Malta's sister island of Gozo to form this comprehensive travel guide
- Best Beaches in Malta - a thorough beach guide covering the most popular spots and plenty of hidden gems
- Accommodation resources: Looking for places to stay? Read my guide to finding where to stay in Malta. Or, for a unique stay, check out this list of great Boutique Hotels in Gozo and more Boutique Hotels in Valletta.