10 Stunning Places to Visit by Yacht in Malta and Gozo

Malta and Gozo are small on paper and enormous from the water. The archipelago is barely thirty kilometres end to end, but the coastline folds in on itself in caves, harbours, salt pans and limestone arches that are almost impossible to read from a road map. A yacht turns the islands into a single, continuous itinerary instead of a list of car parks.

This guide pulls together ten of the most rewarding places to visit Malta by water, from the headline anchorages around Comino to the quiet Gozo coves that most visitors never reach. We charter these waters every week of the season, so the timings, anchorages and route notes below are the ones we actually give to guests on the morning of departure. If you are still weighing up a luxury yacht charter Malta, this should give you a realistic picture of what one good day on the water actually looks like.

1. Blue Lagoon, Comino

The Blue Lagoon is the postcard everyone has already seen, and it earns the reputation. The shallow channel between Comino and Cominotto sits over white sand, which turns the water an almost luminous turquoise on a sunny day. From a yacht you anchor in the deeper edge of the bay and tender in, which keeps you out of the swim zone the day boats use.

Timing is everything here. Between roughly eleven and four the lagoon fills with ferries and party boats from Sliema and Buġibba. If you arrive before nine you usually have it almost to yourself, and the same is true after five when the last cruise leaves. A morning swim before the ferries arrive is one of the simplest luxuries the Mediterranean offers.

The Blue Lagoon suits almost any boat. A flybridge motor yacht gives you the best sun deck for the long anchor, while a sailing yacht reads the tighter parts of the channel comfortably. Either way, plan a tender for the run into the swim line.

2. Crystal Lagoon and the Comino caves

Five minutes around the headland from the Blue Lagoon, the Crystal Lagoon is the quieter sibling. The water is deeper, the cliffs are higher, and the colour shifts from turquoise to a darker glassy blue that photographs almost black at the edges. There is no beach here, so the day boat traffic is much lighter.

This is the best snorkelling stop on the Comino circuit. The cave network along the south of the island is shallow enough for confident swimmers and dramatic enough for a tender tour with non swimmers on board. We usually drop a paddleboard and a couple of seabobs from our water toys range here, because the bay rewards exploration in a way the Blue Lagoon does not.

If your group is mixed in confidence, anchor on the eastern edge and use the tender to ferry people in and out of the caves. The light inside Santa Marija cave at midday is the moment most guests reach for a camera.

The Crystal Lagoon is where I send guests who think they have already done Comino. The light in those caves is genuinely different from the lagoon next door.

3. Valletta and the Grand Harbour

Approaching Valletta by water is one of the great Mediterranean entrances. The bastions rise straight out of the harbour, the limestone glows ochre in the late afternoon, and the scale of the fortifications only makes sense once you are below them on a deck. Cruise ships try to mimic this view but they sit too high to feel it properly.

The Grand Harbour itself is working water. Tugs, ferries, naval craft and the occasional super yacht all share the basin, so movements need to be coordinated with port control. Most charters do a slow loop past Fort St Angelo and the Three Cities, then exit without docking unless lunch in Birgu is part of the plan.

If your booking is a half day rather than a full day, this is the route to choose. A two hour Grand Harbour run from Sliema covers more visual ground than an entire afternoon of Valletta walking tours, and it ends with the same sunset light hitting the bastions from the water side.

4. Marsamxett Harbour and Manoel Island

Marsamxett is the harbour on the other side of the Valletta peninsula, and it is often skipped by guests who only know the Grand Harbour name. That is a mistake. The Sliema waterfront, Manoel Island fort and the back side of the Valletta bastions all sit inside this basin, and the light here in the morning is softer than across the headland.

Most Sliema based charters start and end inside Marsamxett, which makes it the easiest harbour to use as a working base. There is good shelter from a north westerly, decent depth for anchoring close in, and a steady supply of small craft that means traffic is rarely an issue. The view of the Valletta skyline from Manoel Island at golden hour is one of the most photographed in the Mediterranean for a reason.

For groups who want a slow start, a coffee at anchor in Marsamxett before pushing north is a small ritual we recommend often. The harbour acts as a natural warm up for the rest of the day.

5. Mġarr ix-Xini, Gozo

Mġarr ix-Xini is a narrow finger of water cut into the south coast of Gozo, with cliffs on both sides and a tiny pebble beach at the head. It is the kind of place that does not appear on most itineraries, which is precisely why it earns a slot on this one. The bay holds about five yachts comfortably and feels empty even when it is full.

There is one small restaurant at the head of the bay, family run, that has fed sailors for decades. A long lunch there with the tender pulled up on the pebbles is one of the most authentic Gozo boat trip experiences available, and it costs less than most of the equivalent waterfront restaurants in Sliema. Book ahead in summer because the terrace is small.

Mġarr ix-Xini is best approached in calm weather. A southerly swell rolls straight into the entrance and makes the anchorage uncomfortable, so we will route you elsewhere if the forecast is wrong. On a settled day it is one of the quiet highlights of the islands.

I check three forecasts before I commit to the south of Gozo. When the weather lines up, Mġarr ix-Xini is one of the calmest lunch stops in the Mediterranean. When it does not, we go north.

6. Dwejra Bay and the Inland Sea, Gozo

Dwejra is the geological showpiece of Gozo. The Azure Window collapsed in 2017, but the bay around it is still full of the features that made the area famous. The Fungus Rock sits offshore, the Inland Sea connects to the open water through a tunnel in the cliff, and the limestone pavements between them photograph beautifully in low sun.

From a yacht you can anchor outside Dwejra in calm conditions and tender to the small cove. Local boats run through the Inland Sea tunnel, which is too tight for anything larger than a tender, and the experience of passing through the cliff into the sheltered pool on the other side is one most visitors do not realise is possible.

Dwejra is a north westerly weather call. The bay is exposed and gets uncomfortable quickly when the wind builds, so we treat it as a morning stop on a settled day rather than a guaranteed slot in every itinerary. When it works it is unforgettable.

Stops on the route

7. Ramla Bay, Gozo

Ramla is the red sand beach on the north coast of Gozo, and it is one of the most striking colour contrasts in the Maltese islands. The sand has a rust orange tone that sits against the deep blue water in a way no other beach in the archipelago matches. Approaching it from the sea is the best angle on it.

There is no harbour here. Yachts anchor offshore in the sand patches and tender in for a swim or a walk up to the Calypso cave on the headland above the beach. The water is shallow well out from the shore, so it is one of the friendliest anchorages for guests with small children or anyone learning to use a paddleboard.

Ramla pairs naturally with Mġarr ix-Xini for a Gozo day. South coast lunch, north coast swim, and the crossing back to Comino in the late afternoon. The salt pans north of Marsalforn are worth a slow pass on the way if your captain has time, because the geometry of the rectangles only works from the water.

8. St Paul's Bay and Mellieħa Bay

Back on the Malta side, the north coast curves into two large, shallow bays that are popular with locals and quiet on a yacht. St Paul's Bay is the larger of the two, with the small island of St Paul at its mouth and a wide sandy bottom that holds an anchor reliably. Mellieħa Bay sits just to the west, with one of the longest sandy beaches in Malta running across its head.

These are the calmest anchorages on the Malta side in a southerly wind, which makes them an important option when the Comino crossing is uncomfortable. Most days the water in Mellieħa Bay is flat enough for a long paddleboard run along the beach, and the temperature climbs a degree or two above the open sea by mid afternoon.

The bays are also the right call for a relaxed end to a long charter day. After the Comino circuit and a Gozo crossing, an hour at anchor in Mellieħa with the engines off is the moment most guests realise they have not looked at their phone since lunch.

The best mornings on the water are the ones that start before the rest of the islands wake up. We push off at seven and have the Blue Lagoon to ourselves for an hour. That hour sells more repeat charters than any brochure we have ever printed.

9. Il-Ħofriet and the hidden coves

Il-Ħofriet is the local name for a stretch of coves on the south east coast of Malta, between Marsaskala and Marsaxlokk. It is rarely on a tourist map and almost never on a brochure, which is part of the point. The coast here is low limestone with shallow inlets, swimming pools cut into the rock and tiny natural arches that yachts can drift past without anchoring.

The route from Marsamxett south past Valletta and around the south east corner takes about two hours at cruising speed. Most charters that include this section do so on a longer day or as a dedicated south coast itinerary, because it makes more sense to commit to the area than to add it as a side trip. The water here is exceptionally clear because the bottom is rock rather than sand.

Il-Ħofriet is the answer for guests who have already done the headline spots. If you are interested in this kind of routing, our piece on hidden gems Malta by yacht covers more of the same coast in detail, including the smaller landings near Delimara.

10. Wied il-Mielaħ window, Gozo

Since the Azure Window collapsed, Wied il-Mielaħ has quietly taken over as the most photogenic limestone arch in Gozo. The window sits on the north west coast, framed by sheer cliffs and reached most easily by tender from a yacht anchored offshore. The drive by road is long and the parking is limited, so the boat approach is genuinely the better one.

There is no swimming through the arch, but the cliffs around it hide several small caves that are worth exploring with snorkels. The water here is deep, clear and cold in places where the cliff overhangs cut the sun. It is a five star tender hour rather than a long anchor, and we usually combine it with Dwejra to get a full north west Gozo morning.

Wied il-Mielaħ is the kind of stop that makes guests start to plan the next charter before this one is over. It also rounds out a list of Malta coastal attractions that go far beyond the Blue Lagoon, which is the point of building an itinerary on the water in the first place.

How to plan a one day Malta + Gozo route

• Start in Marsamxett or Sliema by half past eight at the latest. The first hour of the day is the most useful one on the water, especially in summer.
• Cross to the Blue Lagoon mid morning, before the day boats arrive. Plan to leave by half past eleven if you want to escape the lunchtime crowd.
• Pivot through the Comino caves and Crystal Lagoon for a snorkel stop, then cross the Gozo Channel for lunch at Mġarr ix-Xini or a Mġarr harbour anchorage.
• Use the afternoon for either Ramla and the north Gozo coast, or Dwejra and Wied il-Mielaħ if the wind is from the south.
• Drift home along the Comino south coast in the late afternoon, with a final swim stop somewhere quiet before pushing back to Marsamxett for sunset.

Most of our day charters follow some version of this route, adjusted to the wind on the morning. If you want to see the kind of yacht that handles it well, our experiences collection groups the boats by typical itinerary rather than by length, which is usually a more useful way to choose.

Putting the route together

Malta is one of the rare destinations where the headline spots and the quiet ones sit close enough together to fit into the same charter day. The Blue Lagoon, Grand Harbour and Wied il-Mielaħ are not three days of sightseeing on land. From the water they are three stops on a single coastal loop, with the tender doing the work that a hire car would normally take a week to deliver.

Build the day around timing rather than distance. Push off early, anchor in the busy spots before the day boats arrive and use the quiet hours of the afternoon to find the coves that do not appear on any list. That is the version of the islands that turns a one off booking into a yearly habit, and it is the version we hope you have on your first day on the water with us.