Mellieha is a fantastic base for boat tours and cruises because of its proximity to some of Malta’s most beautiful coastlines and islands. The calm waters and stunning scenery make it ideal for exploring by sea. Whether you’re after a quick trip to Blue Lagoon or a full-day sailing adventure, Mellieha offers a variety of options for every type of traveler. We particularly like the Comino & Gozo: Blue & Crystal Lagoons Cruise with Sea Caves because it combines snorkeling, scenic stops, and a small-group experience that feels intimate and relaxing. If you’re after a longer, more leisurely day, the Three Bay Cruise including the Blue Lagoon is perfect for soaking up the sun and enjoying multiple stops.
In this guide, we’ve compiled the best boat tours and cruises in Mellieha ranging from half-day jaunts to private full-day charters. Each offers a unique way to experience Malta’s coastal beauty, with some focusing on snorkeling and swimming, others on sightseeing, and a few offering the privacy of your own boat.
1. Comino & Gozo: Blue & Crystal Lagoons Cruise with Sea Caves
At number 1 on our list, this half-day or sunset cruise from Mellieha takes you to the Blue Lagoon, Crystal Lagoon, and the enchanting sea caves around Comino. The tour is renowned for its personalized small-group experience with only 25 passengers aboard, making it one of the most intimate options available. You’ll explore scenic spots like St. Maria Bay and Gozo Harbour, with plenty of chances to swim and snorkel in the pristine turquoise waters. The itinerary includes visits to Mgarr Harbour, San Niklaw Bay, and Santa Maria Caves, with stunning photo stops along the way.
Guides are praised for their friendliness and professionalism, and reviews highlight how the limited group size means more time at each location and less chaos. The tour’s mix of snorkeling, sightseeing, and cave exploring, combined with the stunning coastline, makes it a top choice. It’s especially suited for travelers who value a small, relaxed experience and want to avoid crowded boats.
Bottom Line: An excellent choice for those seeking a personal, well-paced cruise with plenty of swimming and cave exploration.
2. From Mellieha: Three Bay Cruise including the Blue Lagoon
At number 2, this 6-hour day trip offers a classic Malta boat experience with time to swim, snorkel, and relax. Departing from Mellieha, the cruise visits the famous Blue Lagoon, Crystal Lagoon, and Ħalfa Rock Bay. The tour’s highlight is the scenic cruise around Comino and Gozo, with ample time to soak up the sun on deck or take a leisurely swim in the crystal-clear waters. The Blue Lagoon is known for its incredibly vivid blue hues, and the tour allows guests to enjoy free time to explore the shoreline or snorkel among marine life.
Reviewers love the smaller boat size and friendly staff, making for a relaxing and personable experience. The cruise is ideal for those who want a full day of swimming, snorkeling, and sunbathing without the crowds of larger tours. The optional swim stop at Blue Lagoon is a major draw for many.
Bottom Line: Perfect for travelers who value a longer, relaxed day with plenty of swimming and a friendly atmosphere.
3. Comino Blue Lagoon & Crystal Lagoon – 3 Bay Cruise
Number 3 offers a 6-hour cruise that explores three bays, including Crystal Lagoon, Blue Lagoon, and Gebla Tal Halfa. The boat capacity is intentionally limited to 45 passengers to ensure comfort and space. This tour is praised for its comprehensive itinerary, which includes swimming, snorkeling, and sightseeing at each bay, as well as visits to Santa Maria Caves and Elephant Rock.
Guests appreciate the large boat size (70 people capacity) but note that they are limited to 45, which keeps the experience less crowded. The scenic cruise along the coast offers plenty of photo opportunities, and the snorkeling stops are particularly well-rated. Some travelers mention that the inside amenities, like restrooms and shade, add comfort during the longer day.
Bottom Line: Great for those seeking a full-day tour with ample swimming and cave exploration in spacious comfort.
4. Comino: Blue Lagoon, Crystal Lagoon and Sea Caves Boat Tour
Number 4 is a 3-4 hour scenic cruise focusing on the iconic sights around Comino. The boat is cozy, with only 24 people, which makes for a more relaxed and intimate experience. The tour hits all major spots, including Blue Lagoon, Crystal Lagoon, Santa Maria Bay, and the Elephant Rock. Along the way, you’ll get to snorkel in crystal-clear waters and see sea caves and rock formations.
Reviews point out the friendly crew and the small group size as major advantages. The itinerary offers multiple stops for swimming and snorkeling, and the scenic coastal views are breathtaking. The tour is ideal for travelers seeking a shorter, personalized experience that emphasizes snorkeling and sightseeing without the crowds.
Bottom Line: A perfect quick but personal trip to see Malta’s most beautiful coves and caves with plenty of swimming.
5. From Mellieha Bay: Gozo & Blue Lagoon Boat Tour w/ Swim Stop
Ranked 5, this 6.5-hour tour is a comprehensive trip that combines visits to the islands of Malta, Gozo, and Comino. Starting from Mellieha Bay, it includes a walk through Gozitan villages and a swim stop at Blue Lagoon. You’ll get to explore the Old Citadel of Gozo, learn about local culture, and enjoy a cruise around caves accessible only by sea.
Reviewers mention the friendly crew and beautiful scenery as highlights. The tour is well-suited for travelers interested in both cultural sights and swimming, providing a balanced day that showcases Malta’s diverse coastline and islands.
Bottom Line: Best suited for those who want a combination of sightseeing and swimming, with a taste of Gozitan culture.
6. Mellieha: Round Comino, Blue Lagoon & Gozo Cruise with Water
Number 6 offers a 4-hour cruise focusing on scenic highlights and fun water activities. The tour visits Comino’s Blue Lagoon and Crystal Lagoon, with the added bonus of a water slide and complimentary mineral water throughout. The cruise is designed for fun, with snorkeling, swimming, and relaxing on the boat.
Guests love the informal vibe, water slide, and scenic coastline. It’s an excellent choice for families or those wanting a shorter, lively adventure that combines sightseeing with water-based fun.
Bottom Line: Suitable for families and travelers seeking an energetic, activity-filled cruise.
7. From Mellieha Bay Malta: Blue Lagoon Sunset Cruise
Number 7 features a sunset experience departing at 4:00 PM. It includes 1.5 hours of swimming and snorkeling at the Blue Lagoon and ends with watching the sunset, with complimentary prosecco in hand. The relaxed, evening atmosphere is perfect for romantic getaways or anyone wanting a quieter, more atmospheric experience.
Reviews highlight the beautiful sunset views and chilled music, making it a memorable way to end the day. The tour is best suited for those wanting to avoid daytime crowds and enjoy a peaceful, scenic evening.
Bottom Line: An ideal choice if you want to combine swimming with a romantic sunset view.
8. Comino: Mystic Caves, Blue and Crystal Lagoon Boat Cruise
Number 8 is a private 1-hour boat tour perfect for small groups wanting a personalized experience. It explores Comino’s caves, Blue Lagoon, and Crystal Lagoon, with the option to snorkel and view caves like Lover’s Cave and Roofless Cave.
Reviews mention the calm, cosy boat and friendly skipper, making it ideal for travelers who prefer a more intimate outing. The tour is flexible and can be adapted to your interests, making it great for a quick, customized exploration.
Bottom Line: Best for private groups or couples looking for a short, personalized boat experience.
9. Comino Splash & Dash: Private Blue/Crystal Lagoon Boat Tour
At number 9, this 2-hour private tour focuses on secluded beaches and caves. It offers the chance to skip lines, access hidden beaches, and snorkel in calm waters. The itinerary includes stops at Crystal Lagoon, Cominotto, and the Blue Lagoon, with options for sailing, swimming, and marine viewing.
The private nature makes it ideal for families or couples wanting a customized, peaceful outing. The reviews emphasize how the skipper’s flexibility and the secluded spots make this tour a truly special experience.
Bottom Line: Perfect for those wanting privacy and exclusivity while exploring Malta’s coastal secrets.
10. Malta, Gozo, and Comino: Full Day Sailing Charter
Number 10 offers an 8-hour private sailing experience aboard a 14-meter sailboat. You’ll drop anchor at scenic spots, swim, snorkel, paddleboard, and relax with your friends or family. The guide, Peter, is praised for his attentiveness and taking guests to gorgeous, lesser-known locations.
This tour is ideal for adventurers wanting a private, flexible day on the water. The sailing, swimming, and flexible itinerary make it a memorable day for those who love being on the water with a personal touch.
Bottom Line: Excellent for small groups seeking a custom, full-day sailing adventure.
11. Malta, Gozo, and Comino: Half Day Sailing Charter
Ranked 11, this 4-hour private trip offers similar perks to the full-day but in a shorter time frame. It’s perfect for families or couples who want to sail, swim, and enjoy the scenery without committing a full day.
Guests mention the welcoming crew and beautiful spots, along with the ability to bring your own food and use paddleboards and snorkel gear. It’s a flexible way to enjoy Malta’s waters in a personalized setting.
Bottom Line: Ideal for shorter, private outings focused on relaxation and exploration.
12. Private 8-hour Tour to Valletta, Marsaxlokk & Mdina
This private land and sea combo tour combines the cultural highlights of Valletta and Mdina with a cruise. It includes city tours, a visit to a fishing village, and free time for lunch in Marsaxlokk. It’s perfect for travelers wanting an all-in-one experience.
Reviews praise its flexibility and the personalized attention. It’s suited for those who want more control over their day and enjoy both sightseeing and a boat ride.
Bottom Line: Best for travelers who want a comprehensive, customizable day combining land and sea.
How to Choose the Right Boat Tour in Mellieha
When selecting a tour, consider your budget, time availability, and interests. For short trips with snorkeling, tours like Comino & Gozo: Blue & Crystal Lagoons Cruise or Comino: Blue Lagoon, Crystal Lagoon and Sea Caves Boat Tour are excellent. If you prefer a full day of sailing with more flexibility, the Full Day Malta & Gozo Sailing Charter is perfect.
For private experiences, options like Comino Splash & Dash and Private 8-hour Malta & Comino Tour provide tailored outings. Budget travelers should look at smaller group tours, while romantics and families might prefer sunset cruises or private charters.
Booking early is advisable, especially in peak summer months, to secure your preferred time and boat size. Also, consider the weather—Malta’s sea conditions are generally calm in summer, making these tours more enjoyable.
In summary, Mellieha offers a wide array of boat trips—from quick cave explorations to luxurious private sailing. If you’re looking for a relaxed, scenic cruise, tours like the Three Bay Cruise are perfect. For those wanting privacy or customization, private options such as the Full Day Private Boat Charter deliver a tailored experience. Whatever your style, booking early ensures you won’t miss out on exploring Malta’s stunning waters.
Enjoy your time on the water, and don’t forget your snorkel!