Malta Yacht Charter Routes: Best Bays and Anchorages

8 min read · Published: October 24, 2024 · Updated: October 29, 2026 · Prices and details checked: October 2026

The best yacht charter route in Malta follows the wind, not a fixed list: Comino’s lagoons and Gozo’s south coast on calm or northerly days, Mellieha Bay and St Paul’s Islands when the westerly blows, and Marsaxlokk for a sheltered night in the south east. Every bay lies within a day’s sail of the marinas at Msida, Portomaso and Mgarr, so you rarely need to commit to a plan before breakfast.

Table of contents

1. Which bays should a Malta yacht charter include?
2. When is the Blue Lagoon worth it, and when is the Crystal Lagoon better?
3. What does the south coast of Gozo offer a sailing route?
4. Where do you anchor when the wind blows from the west?
5. Why should Marsaxlokk be on a route around southern Malta?
6. How do you plan each day around the wind?
7. FAQ

Which bays should a Malta yacht charter include?

A good charter route touches four areas: Comino, the south coast of Gozo, the bays of northern Malta between Mellieha and St Paul’s Bay, and the south east around Marsaxlokk. Comino is the postcard stop, Gozo has the clearest water and highest cliffs, northern Malta the widest sandy bays and most reliable shelter, and the south east a working fishing harbour with calm anchorages behind Delimara Point.

With a single day you will spend it on Comino, with a weekend add Gozo, and with a week you can sail the whole circuit. Our guide on what to know before chartering in Malta covers licences, skippers and what the price includes.

When is the Blue Lagoon worth it, and when is the Crystal Lagoon better?

The Blue Lagoon is worth it early in the morning and after the ferries leave; in the middle of the day the Crystal Lagoon on Comino’s south coast is the better anchorage. Switching between them costs little time.

The Blue Lagoon sits between Comino and the islet of Cominotto. The sand bottom turns the water a pale turquoise no other bay in Malta matches, and the shallow channel is ideal for swimming straight off the stern. The drawback is company: ferries from Marfa and Cirkewwa arrive from the morning roughly every half hour, and the return boats leave until around 17:00. A charter yacht can be at anchor before the first boat arrives and stay after the last one has gone, and the sunset behind Gozo from here is the best in the islands.

The Crystal Lagoon lies on the south side of Comino, facing Malta. It is a rocky inlet with deeper water, caves in the cliff walls and far fewer visitors. The depth means more anchor chain, but the reward is clear water for snorkelling along the rock faces and shade from the cliffs in the afternoon. In a northerly wind the island blocks the swell and this is the more comfortable of the two. Santa Marija Bay on the north coast is a third option with a small sandy beach, useful when the wind is from the south.

What does the south coast of Gozo offer a sailing route?

Gozo’s south coast offers the best snorkelling water in the archipelago and natural shelter from the prevailing north westerly. Aim for Mgarr ix-Xini and Xlendi.

Mgarr ix-Xini is a narrow inlet cut deep into the limestone, with calm water even when there is a chop outside and rock walls that drop steeply into the sea. A pebble beach and a seasonal restaurant sit at its head. Swing room is limited, so arrive early in high season.

Xlendi is a village bay further west, with a short sandy beach, a promenade of restaurants and a watchtower on the headland. Going ashore for dinner is easy, the cliffs either side of the entrance are good for snorkelling, and the bay faces south west, which gives a direct view of the sun going into the sea. It is open in that direction too, so check the forecast before staying overnight. Between the two bays the Ta’ Cenc cliffs are best seen from the water.

Where do you anchor when the wind blows from the west?

When the wind is from the west or south west, head for Mellieha Bay or the anchorage behind St Paul’s Islands on Malta’s north east coast. Both are sheltered by the land to the west and give flat water when the Comino side is uncomfortable.

Mellieha Bay is the largest sandy bay in Malta. The water shallows gradually over sand, which makes anchoring simple and swimming easy for children. It is a resort beach, not a wilderness stop, but as a safe anchorage in a westerly it has few rivals. It is open to the north east, so avoid it when the Grigal, the north easterly, is blowing.

St Paul’s Islands are two islets off the headland between St Paul’s Bay and Mellieha, where tradition places the shipwreck of St Paul; a statue of the saint stands on the larger one. The channel between the islets and the mainland gives a quiet anchorage with rocky snorkelling along the shore, and it is a convenient swim stop between Comino and the marinas at Msida or Portomaso.

Why should Marsaxlokk be on a route around southern Malta?

Marsaxlokk is the best overnight anchorage on Malta’s south east coast and the natural stop on any route that rounds the island rather than only shuttling between the marinas and Comino. The bay is large, mostly sheltered, and puts a village with fish restaurants a short dinghy ride from the boat.

The village is a working fishing harbour where the painted luzzu boats are moored, the quay fills with market stalls on Sunday mornings, and the waterfront restaurants serve what the boats brought in.

The Delimara peninsula on the east side of the bay has small rocky inlets facing south. Il-Hofra l-Kbira and Il-Hofra z-Zghira are the main ones, with clear water, flat rock for sunbathing and good snorkelling along the edges, and they make a fine lunch stop before you move into the main bay for the night. The area is open to the south east, so if the Xlokk, the humid south easterly, is forecast, choose the other side of the island.

How do you plan each day around the wind?

Check the forecast each morning and pick the side of the islands that is in the lee. The prevailing wind is the north westerly, called the Majjistral, and most summer days follow it, which is why Gozo’s south coast and the Crystal Lagoon are the default anchorages.

A rule of thumb for the main bays:

• North westerly (most common): Crystal Lagoon, Mgarr ix-Xini, Xlendi, the Delimara inlets.
• Westerly or south westerly: Mellieha Bay, St Paul’s Islands, Santa Marija Bay.
• North easterly (Grigal, more frequent outside high summer): Marsaxlokk, Mgarr ix-Xini, the south side of Comino.
• South easterly (Xlokk): the Blue Lagoon, Mellieha Bay, the north coast of Gozo.

A skipper knows these choices by heart, but understanding them explains why a planned stop sometimes gets swapped at short notice. On a bareboat the decision is yours, and there is always a coast facing away from the wind.

One note on snorkelling, whichever bay you end up in: Malta is about rock, not reef. Fish gather along the cliff bases and in the caves, and the clarity of the water is the attraction. Bring your own mask and fins if the charter does not supply them, and go in the morning or late afternoon, when the day boats have thinned out.

FAQ

Start with the forecast, pick the sheltered coast, and let the islands do the rest. If you would like help arranging a skippered or bareboat charter from Malta, or an apartment in Sliema or St Julian’s for the nights before and after, send us a booking request and we will put a route together with you.

Image credits: Pexels; Pixabay / raiKom; Pixabay / Efraimstochter