Best Boat Trips in Malta: Harbors, Lagoons & Caves

Malta is best understood from the water. Whether you want to drift through sea caves glowing electric blue, anchor above the clearest lagoon in the Mediterranean, or cruise past 700 years of Grand Harbour fortifications, these are the boat trips worth planning your days around.

Aerial view of boats anchored in a clear turquoise lagoon surrounded by rugged cliffs and rocky coastline in Malta, inviting exploration and relaxation on the water.

Plan and book this trip

Tools from our partner Travelpayouts help you compare flights and hotels. If you book through them, we may earn a commission at no extra cost to you.

Flights

Hotels map

Few places reward a boat as generously as the Maltese archipelago. Within a 30-kilometre radius, you can swim through limestone sea caves, anchor in water so clear you can count the rocks 10 metres below, and sail past fortress walls that have shaped Mediterranean history for centuries. Whether you have half a day or a full one, these trips span the best of what Malta's coastline, lagoons, and harbours offer. For context on planning your wider time on the island, our 7-day Malta itinerary covers how to sequence these experiences without backtracking. If you're deciding when to go, the best time to visit Malta guide lays out exactly which months keep the seas calm and the crowds manageable.

ℹ️ Good to know

Since May 1, 2025, landing on Comino island requires a pre-booked ticket (QR code) via blcomino.com. If your tour only anchors offshore for swimming, you're exempt. Confirm with your operator before booking.

Comino's Lagoons & Sea Caves

Clear blue lagoon waters with rocky cliffs and visible sea caves on Comino island, Malta, under a sunny sky. — Photo B PJ

The waters around Comino are the centrepiece of Malta's boat trip scene, and for good reason. The lagoons here rank among the most photogenic in the entire Mediterranean, and the caves along the northern coastline add an entirely different dimension to a half-day on the water. Most tours from Valletta, Sliema, or the Cirkewwa ferry terminal reach Comino in 20-40 minutes, making it a natural anchor for any boat excursion.

Two blue-striped deck chairs on rocky shore overlooking the turquoise waters and rugged cliffs of the Blue Lagoon, Comino under a bright sky.

1. Anchor in the Blue Lagoon, the Mediterranean's Most Photographed Water

Tours typically anchor here for 60-75 minutes. Arrive on the first morning departure (around 09:00) to beat the crowds. Afternoon visits in July and August bring hundreds of boats. The colour is real — and worth it if you time it right.

1. Anchor in the Blue Lagoon, the Mediterranean's Most Photographed Water

Tours typically anchor here for 60-75 minutes. Arrive on the first morning departure (around 09:00) to beat the crowds. Afternoon visits in July and August bring hundreds of boats. The colour is real — and worth it if you time it right.

Two blue-striped deck chairs on rocky shore overlooking the turquoise waters and rugged cliffs of the Blue Lagoon, Comino under a bright sky.

Dramatic view of Crystal Lagoon with turquoise water, rocky cliffs, and several boats anchored in the tranquil bay under a clear blue sky.

2. Swim the Crystal Lagoon and Its 30-Metre Boulder Tunnel

Most full-day Comino tours include a 30-minute stop here after the Blue Lagoon. The 30-metre underwater boulder tunnel and sea caves draw snorkelers and divers. Far fewer boats anchor here, making it the quieter, more rewarding half of the same trip.

2. Swim the Crystal Lagoon and Its 30-Metre Boulder Tunnel

Most full-day Comino tours include a 30-minute stop here after the Blue Lagoon. The 30-metre underwater boulder tunnel and sea caves draw snorkelers and divers. Far fewer boats anchor here, making it the quieter, more rewarding half of the same trip.

Dramatic view of Crystal Lagoon with turquoise water, rocky cliffs, and several boats anchored in the tranquil bay under a clear blue sky.

Santa Marija Bay shoreline with sandy beach covered in seaweed, calm turquoise water, and rocky hills under a cloudy sky at dusk.

3. Dock at Santa Marija Bay for Shade, Shallow Water & Calm

Boats that land on Comino often use Santa Marija Bay as the disembarkation point. Tamarisk trees provide natural shade, and the shallow turquoise water is ideal for families. The 17th-century chapel above the shore takes five minutes to walk up to.

3. Dock at Santa Marija Bay for Shade, Shallow Water & Calm

Boats that land on Comino often use Santa Marija Bay as the disembarkation point. Tamarisk trees provide natural shade, and the shallow turquoise water is ideal for families. The 17th-century chapel above the shore takes five minutes to walk up to.

Santa Marija Bay shoreline with sandy beach covered in seaweed, calm turquoise water, and rocky hills under a cloudy sky at dusk.

Sea Caves Along Malta's Coastline

Aerial view of Malta’s rugged coastline with a prominent natural sea cave arch, clear turquoise water, and a small boat nearby. — Photo Mihai Vlasceanu

Malta's limestone cliffs have been hollowed by centuries of wave action into some of the most striking sea caves in the Mediterranean. The Blue Grotto on the southern coast is the most famous, but Gozo's west coast at Gozo offers its own extraordinary underwater geology at Dwejra. For divers, our Malta diving guide covers both sites in detail, including how to reach the underwater sections only accessible by boat.

A wide view of Malta’s Blue Grotto showing dramatic limestone cliffs, a large sea arch, turquoise blue water, and coastal plants in the foreground.

4. Ride a Traditional Luzzu Into the Blue Grotto Sea Caves

Small traditional boats depart from Wied iż-Żurrieq year-round, weather permitting. The bioluminescent blues inside peak in morning light before 10:00. The ride costs around €10 per person (cash only) and takes 20-25 minutes. Conditions are checked daily — don't visit if seas are rough.

4. Ride a Traditional Luzzu Into the Blue Grotto Sea Caves

Small traditional boats depart from Wied iż-Żurrieq year-round, weather permitting. The bioluminescent blues inside peak in morning light before 10:00. The ride costs around €10 per person (cash only) and takes 20-25 minutes. Conditions are checked daily — don't visit if seas are rough.

A wide view of Malta’s Blue Grotto showing dramatic limestone cliffs, a large sea arch, turquoise blue water, and coastal plants in the foreground.

Overhead view of the Blue Hole at Dwejra, Gozo, showing clear blue water surrounded by rugged limestone formations.

5. Take a Boat Into Dwejra's Inland Sea on Gozo's Wild West Coast

Local fishermen run short boat trips from the Inland Sea through a narrow tunnel in the cliffs to the open water where the Azure Window once stood. The trip lasts 15-20 minutes and costs a few euros. The geology here is unlike anything else in the archipelago.

5. Take a Boat Into Dwejra's Inland Sea on Gozo's Wild West Coast

Local fishermen run short boat trips from the Inland Sea through a narrow tunnel in the cliffs to the open water where the Azure Window once stood. The trip lasts 15-20 minutes and costs a few euros. The geology here is unlike anything else in the archipelago.

Overhead view of the Blue Hole at Dwejra, Gozo, showing clear blue water surrounded by rugged limestone formations.

Wied il-Għasri gorge with turquoise water flowing between rugged limestone cliffs under a bright sky on Gozo’s north coast.

6. Kayak or Swim Into Wied il-Għasri, Gozo's Secret Limestone Gorge

This narrow gorge on Gozo's north coast is most dramatic when approached by kayak from the sea. The gorge walls rise steeply on both sides, and the water is calm and clear. No tour boats; you'll need a kayak rental or guided sea-kayaking trip from nearby Marsalforn.

6. Kayak or Swim Into Wied il-Għasri, Gozo's Secret Limestone Gorge

This narrow gorge on Gozo's north coast is most dramatic when approached by kayak from the sea. The gorge walls rise steeply on both sides, and the water is calm and clear. No tour boats; you'll need a kayak rental or guided sea-kayaking trip from nearby Marsalforn.

Wied il-Għasri gorge with turquoise water flowing between rugged limestone cliffs under a bright sky on Gozo’s north coast.

Grand Harbour & the Three Cities

Aerial view of Grand Harbour in Malta showing historic fortifications, marina with many yachts, and golden city buildings. — Photo Polina ⠀

The Grand Harbour is one of the great natural harbours of the world, and seeing it from the water reveals layers of history invisible from the bastions above. The ferry crossing between Valletta and the Three Cities is the simplest and cheapest boat trip in Malta, taking only seven minutes, but longer harbour cruises reveal the full scale of fortifications, dockyards, and wartime history that define this stretch of water.

Crowds watch the noon cannon fire and smoke erupting from the historic Saluting Battery at Upper Barrakka Gardens, overlooking Malta’s Grand Harbour.

7. Depart from Beneath the Upper Barrakka Cannon for a Grand Harbour Cruise

Most Grand Harbour cruises depart from the Valletta Waterfront below the Upper Barrakka Gardens. The noon cannon fires directly above your departure point. Cruises typically run 45-90 minutes and circle past Fort St. Angelo, the Three Cities dockyards, and Valletta's full limestone ramparts.

7. Depart from Beneath the Upper Barrakka Cannon for a Grand Harbour Cruise

Most Grand Harbour cruises depart from the Valletta Waterfront below the Upper Barrakka Gardens. The noon cannon fires directly above your departure point. Cruises typically run 45-90 minutes and circle past Fort St. Angelo, the Three Cities dockyards, and Valletta's full limestone ramparts.

Crowds watch the noon cannon fire and smoke erupting from the historic Saluting Battery at Upper Barrakka Gardens, overlooking Malta’s Grand Harbour.

A panoramic view of Fort St. Angelo jutting into the Grand Harbour, surrounded by deep blue water, boats, and the cityscape of Birgu, Malta.

8. See Fort St. Angelo from the Water on a Grand Harbour Circuit

The view of Fort St. Angelo from the harbour is the most dramatic way to understand why it held during the Great Siege of 1565. Harbour cruises pass within metres of its sea walls. Combine with a visit inside on foot afterward via the Three Cities ferry for a full half-day.

8. See Fort St. Angelo from the Water on a Grand Harbour Circuit

The view of Fort St. Angelo from the harbour is the most dramatic way to understand why it held during the Great Siege of 1565. Harbour cruises pass within metres of its sea walls. Combine with a visit inside on foot afterward via the Three Cities ferry for a full half-day.

A panoramic view of Fort St. Angelo jutting into the Grand Harbour, surrounded by deep blue water, boats, and the cityscape of Birgu, Malta.

Stone watchtower at Gardjola Gardens in Senglea, Malta, with warm evening light and palm trees silhouetted against a clear sky.

9. Cross to Senglea by Dghajsa Ferry and Walk Up to Gardjola Gardens

Traditional dghajsa water taxis still operate between Vittoriosa, Senglea, and the Valletta Waterfront. Crossing takes 5-7 minutes. From the Senglea landing, a short walk brings you to the Gardjola watchtower and one of the Grand Harbour's best views, looking directly back at Valletta.

9. Cross to Senglea by Dghajsa Ferry and Walk Up to Gardjola Gardens

Traditional dghajsa water taxis still operate between Vittoriosa, Senglea, and the Valletta Waterfront. Crossing takes 5-7 minutes. From the Senglea landing, a short walk brings you to the Gardjola watchtower and one of the Grand Harbour's best views, looking directly back at Valletta.

Stone watchtower at Gardjola Gardens in Senglea, Malta, with warm evening light and palm trees silhouetted against a clear sky.

Aerial view of Fort St. Elmo and Valletta’s historic cityscape, surrounded by blue waterfronts and stone ramparts at the tip of the peninsula.

10. View Fort St. Elmo's Sea Walls from a Valletta Harbour Entry

Fort St. Elmo sits at the tip of the Sciberras Peninsula where Marsamxett Harbour and the Grand Harbour converge. Boats entering or leaving Valletta pass within metres of its 16th-century walls. Some evening harbour cruises specifically frame this approach at sunset for maximum effect.

10. View Fort St. Elmo's Sea Walls from a Valletta Harbour Entry

Fort St. Elmo sits at the tip of the Sciberras Peninsula where Marsamxett Harbour and the Grand Harbour converge. Boats entering or leaving Valletta pass within metres of its 16th-century walls. Some evening harbour cruises specifically frame this approach at sunset for maximum effect.

Aerial view of Fort St. Elmo and Valletta’s historic cityscape, surrounded by blue waterfronts and stone ramparts at the tip of the peninsula.

Northern Malta & Coastal Swimming Spots by Boat

A wide bay with clear turquoise water, rocky cliffs, and green hills along Malta's northern coast, perfect for boat trips and coastal swimming. — Photo Ferenc Horvath

Malta's northwest coast offers a string of bays and coves that are far more rewarding when approached by water than by road. Many operators run round-island boat trips that stop at several of these locations in sequence. For a closer look at what awaits onshore, the best beaches in Malta guide covers each bay with practical detail on access and conditions.

Panoramic view of Paradise Bay, Malta, showing turquoise waters, anchored boats, rocky coastline, sandy beach, and nearby buildings under a clear sky.

11. Anchor at Paradise Bay Near Cirkewwa for Clear, Sheltered Water

Most Comino-bound boats pass Paradise Bay on the way north. Some operators include a 30-minute stop here before crossing to the Blue Lagoon. The cove is sheltered, the water clear, and it sees a fraction of the traffic of Comino. A good alternative anchor point on windy days.

11. Anchor at Paradise Bay Near Cirkewwa for Clear, Sheltered Water

Most Comino-bound boats pass Paradise Bay on the way north. Some operators include a 30-minute stop here before crossing to the Blue Lagoon. The cove is sheltered, the water clear, and it sees a fraction of the traffic of Comino. A good alternative anchor point on windy days.

Panoramic view of Paradise Bay, Malta, showing turquoise waters, anchored boats, rocky coastline, sandy beach, and nearby buildings under a clear sky.

Sunset view at Armier Bay, Malta, showing silhouetted people on the beach, boats on calm water, and dramatic clouds overhead.

12. Stop at Armier Bay for a Local Contrast to the Comino Crowds

Round-island boat trips often include Armier Bay as a swim stop on their return from Comino. The smaller rocky cove on the eastern side is better for snorkeling than the main beach. This is local Malta, with fewer tourist boats and more Maltese families mooring their own vessels.

12. Stop at Armier Bay for a Local Contrast to the Comino Crowds

Round-island boat trips often include Armier Bay as a swim stop on their return from Comino. The smaller rocky cove on the eastern side is better for snorkeling than the main beach. This is local Malta, with fewer tourist boats and more Maltese families mooring their own vessels.

Sunset view at Armier Bay, Malta, showing silhouetted people on the beach, boats on calm water, and dramatic clouds overhead.

A sandy stretch of Imgiebah Bay with turquoise waters, small boats anchored offshore, sunbathers, umbrellas, and dry rocky cliffs in the background.

13. Reach Imgiebah Bay by Boat, the Only Practical Way In

There is no easy road to Imgiebah Bay and no facilities onshore. By boat, the approach through sheer limestone cliffs is spectacular, and the small sandy cove is one of the quietest in northern Malta. Best visited on a private charter or small-group sea-kayaking tour.

13. Reach Imgiebah Bay by Boat, the Only Practical Way In

There is no easy road to Imgiebah Bay and no facilities onshore. By boat, the approach through sheer limestone cliffs is spectacular, and the small sandy cove is one of the quietest in northern Malta. Best visited on a private charter or small-group sea-kayaking tour.

A sandy stretch of Imgiebah Bay with turquoise waters, small boats anchored offshore, sunbathers, umbrellas, and dry rocky cliffs in the background.

Clear seawater with swimmers near the rocky entrance of Għar Lapsi cave, surrounded by craggy cliffs on Malta’s southern coast.

14. Snorkel the Sea Caves at Għar Lapsi on Malta's Southwest Coast

Għar Lapsi is a sheltered natural inlet with small sea caves, clear water, and easy access for swimmers arriving by boat. Kayak tours from nearby operators include it as part of a southwest coastal route. The water here is some of the cleanest on the main island.

14. Snorkel the Sea Caves at Għar Lapsi on Malta's Southwest Coast

Għar Lapsi is a sheltered natural inlet with small sea caves, clear water, and easy access for swimmers arriving by boat. Kayak tours from nearby operators include it as part of a southwest coastal route. The water here is some of the cleanest on the main island.

Clear seawater with swimmers near the rocky entrance of Għar Lapsi cave, surrounded by craggy cliffs on Malta’s southern coast.

Gozo Island Boat Excursions

Sunny view of Mġarr Harbour in Gozo with boats docked in the marina and the town rising on the hill behind. — Photo Shell Chapman

Full-day boat trips from Malta frequently include Gozo as a destination, either as a photo stop at Mġarr Harbour or as a disembarkation point for half-day exploration. For anyone spending more time on the island, the Gozo travel guide covers the best ways to use the ferry, hire a car, and structure a day or two around the island's main attractions.

Aerial view of Ramla Bay’s red sand shoreline, gentle blue waves, a solitary statue monument, and scattered greenery along the wide beach.

15. Arrive at Ramla Bay by Boat to Beat the Road Traffic from Victoria

Gozo's only large sandy beach is accessible from the sea on some charter routes. The distinctive red-orange sand and ruins of a Roman villa on the hillside make it a striking approach from the water. Calmer in early morning before the tour buses arrive from Mġarr.

15. Arrive at Ramla Bay by Boat to Beat the Road Traffic from Victoria

Gozo's only large sandy beach is accessible from the sea on some charter routes. The distinctive red-orange sand and ruins of a Roman villa on the hillside make it a striking approach from the water. Calmer in early morning before the tour buses arrive from Mġarr.

Aerial view of Ramla Bay’s red sand shoreline, gentle blue waves, a solitary statue monument, and scattered greenery along the wide beach.

Sunset over Xlendi Bay with calm turquoise water, small boats, and dramatic limestone cliffs framing the narrow inlet.

16. Anchor in Xlendi Bay, Gozo's Most Atmospheric Cliff-Framed Inlet

Private charters and small-group boat tours sometimes anchor in Xlendi's narrow bay for swimming. The cliff walls rise steeply on both sides, and the water drops quickly into serious diving depth. This is one of Gozo's best sites for underwater life directly below the anchor.

16. Anchor in Xlendi Bay, Gozo's Most Atmospheric Cliff-Framed Inlet

Private charters and small-group boat tours sometimes anchor in Xlendi's narrow bay for swimming. The cliff walls rise steeply on both sides, and the water drops quickly into serious diving depth. This is one of Gozo's best sites for underwater life directly below the anchor.

Sunset over Xlendi Bay with calm turquoise water, small boats, and dramatic limestone cliffs framing the narrow inlet.

Wide view of Xwejni Salt Pans with neatly cut limestone pools filled with seawater in the foreground and Gozo's rocky coastline and sea in the background.

17. Pass the Xwejni Salt Pans on a Gozo North Coast Boat Route

The Xwejni Salt Pans along Gozo's north coast are visible from the water on any boat trip rounding the island's eastern or northern shore. The geometric pattern of 300 hand-cut limestone pans is striking from sea level. Best seen on full-day round-Gozo charters.

17. Pass the Xwejni Salt Pans on a Gozo North Coast Boat Route

The Xwejni Salt Pans along Gozo's north coast are visible from the water on any boat trip rounding the island's eastern or northern shore. The geometric pattern of 300 hand-cut limestone pans is striking from sea level. Best seen on full-day round-Gozo charters.

Wide view of Xwejni Salt Pans with neatly cut limestone pools filled with seawater in the foreground and Gozo's rocky coastline and sea in the background.

✨ Pro tip

For Grand Harbour cruises, book the evening departure if available. The light on Valletta's limestone bastions at dusk, with the Three Cities reflected in the water, is consistently better than the midday view.

Scenic Waterfronts to Start or End Your Boat Day

Boats floating on calm water near a historic Maltese waterfront at dusk, with city buildings in the background. — Photo Przemyslaw Smit

Traditional fishing boats float in Spinola Bay, Malta, with colorful buildings, restaurant terraces, and blue water under a partly cloudy sky.

18. Start a St. Julian's Boat Trip from Spinola Bay Among the Luzzu Fishing Boats

Several operators depart from St. Julian's, and Spinola Bay is the staging point. Traditional painted luzzu boats bob in the same water as tour vessels. It's a good spot to arrive 20 minutes early, have a coffee at one of the waterfront cafes, and watch the bay wake up.

18. Start a St. Julian's Boat Trip from Spinola Bay Among the Luzzu Fishing Boats

Several operators depart from St. Julian's, and Spinola Bay is the staging point. Traditional painted luzzu boats bob in the same water as tour vessels. It's a good spot to arrive 20 minutes early, have a coffee at one of the waterfront cafes, and watch the bay wake up.

Traditional fishing boats float in Spinola Bay, Malta, with colorful buildings, restaurant terraces, and blue water under a partly cloudy sky.

View of the Sliema Promenade with modern buildings lining the seafront, people walking along the rocky shore, and waves breaking nearby under a clear sky.

19. Catch a Valletta Ferry from Sliema for the Best Short Harbour Crossing

The Sliema-to-Valletta ferry takes 10 minutes and crosses Marsamxett Harbour with unobstructed views of the city walls in both directions. It costs around €2 each way and runs frequently from early morning. Far more scenic than the bus and a practical start to any Valletta day.

19. Catch a Valletta Ferry from Sliema for the Best Short Harbour Crossing

The Sliema-to-Valletta ferry takes 10 minutes and crosses Marsamxett Harbour with unobstructed views of the city walls in both directions. It costs around €2 each way and runs frequently from early morning. Far more scenic than the bus and a practical start to any Valletta day.

View of the Sliema Promenade with modern buildings lining the seafront, people walking along the rocky shore, and waves breaking nearby under a clear sky.

Traditional brightly painted fishing boats docked along the waterfront in Marsaxlokk, with busy market stalls, cafes, and palm trees in the background.

20. Combine a Sunday at Marsaxlokk Market with a Boat Trip Around Delimara Point

After the Sunday fish market wraps up by midday, some operators offer afternoon boat trips around the Delimara peninsula from Marsaxlokk harbour. The colourful luzzu fleet creates an exceptional backdrop for departure. St. Peter's Pool is a 15-minute ride around the headland.

20. Combine a Sunday at Marsaxlokk Market with a Boat Trip Around Delimara Point

After the Sunday fish market wraps up by midday, some operators offer afternoon boat trips around the Delimara peninsula from Marsaxlokk harbour. The colourful luzzu fleet creates an exceptional backdrop for departure. St. Peter's Pool is a 15-minute ride around the headland.

Traditional brightly painted fishing boats docked along the waterfront in Marsaxlokk, with busy market stalls, cafes, and palm trees in the background.

FAQ

What is the best boat trip in Malta for first-timers?

A full-day Blue Lagoon and Comino cruise is the most rewarding single trip. It typically includes the Blue Lagoon (around 1 hour), Crystal Lagoon (30 min), and sea caves near Comino. Depart on the first morning sailing (around 09:00) to get the clearest water and fewest boats.

Can you visit the Blue Lagoon without a tour?

Yes. You can take the Gozo-Comino ferry from Cirkewwa (near Mellieħa) independently. The ferry runs multiple times daily in summer. As of 1 May 2025, landing on Comino requires a pre-booked ticket via blcomino.com. If you only swim from a boat offshore, no ticket is needed.

How long is the boat trip to the Blue Grotto?

The boat ride itself takes 20-25 minutes and departs from Wied iż-Żurrieq on Malta's south coast. Tickets cost €10 per person (2023 pricing, cash only) and run year-round, weather permitting. Morning trips before 10:00 give the best light inside the caves.

What is the difference between the Blue Lagoon and Crystal Lagoon?

The Blue Lagoon sits between Comino and the Cominotto islet and is the busier, more photographed spot. Crystal Lagoon is on the western side of Comino, quieter, and better for snorkeling due to its underwater boulder tunnel and sea caves. Most full-day tours include both.

What is the cheapest boat trip in Malta?

The Sliema-to-Valletta ferry at around €2 each way is the best-value water crossing on the island. The traditional dghajsa water taxis across the Grand Harbour between Valletta and the Three Cities are a similar price. Blue Grotto cave boat trips at around €10 offer the most dramatic experience for the cost.