Exploring Malta by sea is one of the most magical ways to experience this Mediterranean gem. Whether you’re longing for serene turquoise waters, rugged sea caves, or charming island ports, a private boat trip in Malta puts you in complete control of your adventure. Skip the crowded ferries and rigid schedules; with a boat under your feet and open horizons ahead, every moment can be tailored to your pace and interests.
In this guide, we’ll take you through the top 7 must-see spots that make the best Malta boat tours unforgettable, from iconic snorkelling spots to hidden coves that reflect the sun.
1. Comino’s Blue Lagoon, Nature’s Aquamarine Jewel
No Malta boat adventure is complete without stopping at the legendary Blue Lagoon. With impossibly blue water and soft sandy shallows, it’s perfect for swimming, snorkelling, or just floating beneath the sun. Many travellers head here on larger tour boats, but a Blue Lagoon Malta boat trip means you can linger longer, find quieter coves nearby, and dive into the deep blue whenever you like.
2. Gozo, Malta’s Tranquil Sister Island
Set sail across crystal waters to Gozo, a more peaceful and rural counterpart to Malta. Your Malta boat trip to Gozo can deliver you right to its quaint harbours, where colourful fishing boats bob alongside local cafés offering fresh seafood. Wander the narrow streets of Victoria’s citadel, explore ancient temples, or simply enjoy a seaside lunch before heading back to the water.
A dedicated stop here makes most of the best Malta boat tours truly memorable. Gozo’s relaxed pace and scenic coastline are like stepping into a different world.
3. Comino Coves & Hidden Grottos
Away from the Blue Lagoon’s bustle, Comino’s quieter coves are waiting to be discovered. These tucked-away corners reveal dramatic cliffs, secret sea caves, and quieter anchorages perfect for snorkelling or picnicking on board. If your boat tour allows, drift into a grotto at sunset; the light and reflections are spectacular.
4. Wied iż-Żurrieq & The Blue Grotto
On Malta’s southern coast lies the dramatic Blue Grotto, named for the vibrant play of light across its limestone sea caves. Traditional boats take visitors here for quick tours. Still, on a private voyage, you’ll have the flexibility to cruise the coastline, pause for photos, and even hop in the water to snorkel around the caves, capturing the striking contrast of light and shadow that makes these formations so famous.
5. St. Paul’s Bay & Coral Lagoon
Just north of Malta’s main harbours, St. Paul’s Bay offers a delightful blend of history and sea life. Anchor near the Coral Lagoon and swim among bright fish in clear waters, or relax on deck with views of medieval fortifications. This spot is ideal for nature lovers who want a serene break between stops.
6. Marsaxlokk Bay, Traditional Boats & Coastal Flavours
On the southeastern side of Malta, Marsaxlokk is a colourful fishing village that’s worth visiting by sea. Watch the vibrant luzzus bob against the golden light of early morning, then tie up for a seafood lunch at waterfront eateries. A boat trip to Gozo, with an itinerary that includes this bay, offers both cultural flavour and maritime charm.
7. Ghadira Bay & Mellieħa’s Sandy Shores
If you’re craving a beach moment on your private cruise, head toward the broad sands of Ghadira Bay near Mellieħa. This stretch is perfect for sunbathing or a refreshing swim before continuing your Gozo, Comino, and Blue Lagoon cruise. It’s also a great spot for families or anyone wanting a gentle swim with panoramic island views.
Making the Most of Your Private Boat Trip
While many visitors opt for larger scheduled tours, private boat trips in Malta offer unmatched flexibility: set your own pace, chart your own route, and stop where the mood strikes. Some operators, like GOZOblu Private Boat Tours, specialise in customised itineraries that weave these top highlights into a seamless experience, a great example of how personalised service can elevate your island adventure without feeling salesy.
Pro Tips for a Perfect Sea Day
- Go early to beat the crowds at popular stops like the Blue Lagoon.
- Pack essentials: sunscreen, snorkel gear, water shoes, and plenty of water.
- Check sea conditions, especially if you plan on visiting more exposed spots like the Blue Grotto.
- Local snacks and drinks make for delicious breaks on board.
Why a Private Boat Tour Is the Best Way to See Malta
From turquoise lagoons to silent sea caves, Malta’s islands reward explorers who venture beyond the shore. The freedom of a private boat trip in Malta lets you experience each slice of the Mediterranean at your own pace, from the rustic charm of Gozo to the dazzling waters around Comino and beyond.
Whether it’s your first sea adventure or your tenth, these seven spots are must-see highlights that show off the best of Malta’s coastal magic.
