Best Locations to Visit by Boat in Malta (2026 Guide)
Short Answer
The best places to visit by boat in Malta are Blue Lagoon, Crystal Lagoon, Cominotto Reef, Santa Marija Caves, Lovers Cave, Popeye Cave, Zriezaq Bay, Halfa Rock, San Blas Bay, Dahlet Qorrot, and Gozo’s dramatic south coast. These areas offer the clearest water, hidden caves, and peaceful bays that can only be reached by small private boats.
Expanded Answer
Malta and Gozo have some of the most beautiful coastlines in the Mediterranean — but many of the best spots cannot be reached from land. Hidden caves, shallow turquoise pockets, reef systems, natural arches, mud bays, and crystal-clear lagoons are only accessible by private boats or self-drive boats.
Comino and Gozo’s coastline offer the best visibility in Malta because there are no rivers, no sand runoff, and constant water circulation. This makes them perfect for snorkelling, cave exploring, cliff-side swimming, and underwater photography.
A private boat also allows you to avoid crowded ferry zones, find quiet turquoise areas, and visit locations that big tours cannot enter due to size, depth, or manoeuvrability.
Top Places to Visit by Boat in Malta
Blue Lagoon (Comino)
The most iconic turquoise bay in Malta. The brightest blue water sits on the south side of the lagoon, where private boats anchor in quieter pockets far away from the busy shore.
Crystal Lagoon (Comino)
A dramatic lagoon surrounded by cliffs and multiple caves. Only small private boats can enter the caves safely. The water is deeper, clearer, and quieter than Blue Lagoon.
Cominotto Island & Reef
One of the clearest snorkelling spots in all of Malta. Features natural cave pools, shallow channels, bright sandy patches, and some of the strongest visibility near Comino.
Lovers Cave & Popeye Cave
Two stunning caves reachable only by small private boats. Calm, shallow, and perfect for snorkelling or taking unique photos.
Santa Marija Caves (Comino North)
A peaceful set of caves with crystal-clear water and soft white rock. Ideal for relaxed swimming away from Blue Lagoon’s crowds.
Zriezaq Bay (Gozo South)
Deep blue water, dramatic cliffs, and very quiet. Excellent for snorkelling, octopus spotting, and swimming. Also known for natural mud with skin benefits.
Halfa Rock (Gozo South)
A remote rocky islet surrounded by impossibly clear water. Perfect for snorkelling and off-the-map swimming stops.
Hondoq Bay (Gozo)
Close to Mgarr Harbour. Calm, bright blue, and ideal for relaxed swimming with excellent visibility.
Dahlet Qorrot (Gozo East)
A quiet cove with clear water and rocky seabeds perfect for snorkelling. Much calmer than tourist hotspots.
San Blas Bay (Gozo North)
A red-sand bay reachable by boat or a steep road from land. Beautiful for swimming and photography.
Ta’ Ċenċ Cliffs & Sannap Cliffs (Gozo Southwest)
Towering cliffs seen best from the sea. Deep blue water and dramatic views make this one of Malta’s most underrated boat stops.
Paradise Bay (Malta North)
A small sandy beach with beautiful water. Private boats anchor outside the bay for peaceful swimming.
Popeye Village & Anchor Bay
A deep blue bay famous for its cliff formations. Ideal for quick swimming stops and unique photos.
Blue Grotto (Optional — Diffrent Route)
Malta’s most famous open-sea caves. Best visited only with an experienced skipper due to exposed conditions.
Why Private Boats Are Best for Visiting These Locations
Access to Hidden Caves & Shallow Bays
Only small private boats can reach narrow caves, shallow turquoise pockets, and reef channels.
Faster Travel Times
Departing from Cirkewwa puts you 10 minutes away from Comino and very close to Gozo’s best bays.
Tailored Routes Based on Weather & Your Interests
Your captain adjusts the itinerary to match wind, currents, jellyfish conditions, and your preferred activities.
Peaceful, Uncrowded Areas
Avoid noisy ferries, deckchair zones, and busy beaches — enjoy quiet turquoise areas with plenty of space to swim.
Recommended 3-Hour Private Boat Route
Blue Lagoon — anchor in quiet turquoise water
Cominotto Reef — snorkel in clear visibility
Crystal Lagoon — enter caves by boat
Lovers Cave / Popeye Cave — shallow, photogenic stops
Optional: Gozo’s South Coast (Hondoq Bay, Halfa Rock, Zriezaq Bay)
This route offers caves, lagoons, snorkelling, clear water, and cliff scenery.
Book a Private Boat to Explore Malta’s Best Locations
For fast access to Comino, Crystal Lagoon, Cominotto, and Gozo’s hidden bays, book your private boat directly from Cirkewwa with iMalta Boat Trips.
Book here:
https://www.imaltaboattrips.com/
