Comino is famous for the Blue Lagoon, but there is much more to discover around the island’s coastline.
If you’re searching for secret bays around Comino, quieter swimming spots, or hidden corners away from the busiest areas, exploring by boat gives you a completely different perspective.
Beyond the Blue Lagoon, Comino has recognised bays such as Santa Marija Bay and San Niklaw Bay, the tiny islet of Cominotto, sea caves, rocky inlets and stretches of coastline that are best appreciated from the water. Some places can be reached from land, while others are much easier to explore by boat.
The important thing to remember is that “secret bay” isn’t an official classification. These are simply quieter, lesser-known or less-developed spots around Comino that can offer a more peaceful experience than the island’s famous Blue Lagoon.
And because conditions and crowds change throughout the day, the best place to stop isn’t always the same.
1. Santa Marija Bay: A Quieter Alternative to Blue Lagoon
If the Blue Lagoon is the first place that comes to mind when you think about Comino, Santa Marija Bay offers a noticeably different atmosphere.
Located on the eastern side of Comino, Santa Marija Bay has a sandy beach, natural vegetation and a more relaxed feel than the island’s main attraction. It is also one of Comino’s official bathing areas.
It’s a good option if your group wants to:
- Swim in a more relaxed setting
- Spend some time on a sandy beach
- Snorkel around the rocky edges
- Take a break from the busiest parts of Comino
- Enjoy the landscape without feeling like you’re in the middle of the main tourist hub
Santa Marija Bay isn’t completely unknown or inaccessible, so we wouldn’t describe it as a truly “secret” beach. Its appeal is that it can feel much less intense than the Blue Lagoon, particularly when the main lagoon is busy.
If you’re interested in exploring this part of Comino in more detail, our guide to Santa Maria Bay, Malta, covers what to expect, activities and practical information for your visit.
2. San Niklaw Bay: Another Peaceful Comino Stop
San Niklaw Bay is another recognised bathing area on Comino and is often overlooked by visitors who head straight to the Blue Lagoon.
The bay has sandy sections, rocky and coral outcrops and natural surroundings. Like Santa Marija Bay, it forms part of Comino’s Natura 2000 area and is an official monitored bathing site.
It can make a useful stop on a longer Comino itinerary, particularly if you want to break up the more famous attractions with somewhere that feels a little more relaxed.
The key is not to arrive expecting an untouched beach with nobody around. Instead, think of San Niklaw as one of the quieter alternatives to Comino’s busiest areas.
On a private charter, your skipper can consider the day’s conditions and crowd levels when deciding whether it makes sense to include this area in your route.
3. Cominotto: A Small Islet with Big Blue Waters
Just across the water from Comino is the tiny islet of Cominotto.
The waters around Cominotto are part of the same spectacular marine environment that makes the Blue Lagoon so famous. The area is particularly appealing for swimming, snorkelling and photography when sea conditions are suitable.
Unlike a traditional beach destination, Cominotto is best appreciated from the water.
This is where a smaller private boat has an advantage. You can approach the area, take a swim or snorkel when conditions are appropriate, and then continue along the coastline rather than being tied to one fixed stop.
If you’re deciding between Comino’s two famous lagoons, our Crystal Lagoon vs Blue Lagoon Malta summer guide explains how the two compare, including water depth, crowds, snorkelling and the type of experience each offers.
4. Comino’s Sea Caves and Rocky Coves
Some of the most interesting places around Comino aren’t beaches at all.
The island’s limestone coastline is shaped by caves, arches, rocky inlets and dramatic formations that look completely different from the water.
Some caves are large enough to explore by boat, while others are better viewed from outside. Whether a particular cave is suitable for entering or swimming depends on the conditions, boat traffic, water depth and the skipper’s judgement on the day.
That is important because not every cave you see in a photograph should be treated as a swimming spot.
At GOZOblu, we prefer to choose cave and swimming stops based on the actual conditions rather than promise that a particular location will always be accessible.
A calm morning with light winds can produce a very different experience from an afternoon with stronger swell.
5. Smaller Rocky Inlets: The “Secret” Spots That Change Every Day
This is where things get interesting.
Around Comino, there are countless small sections of coastline that don’t necessarily have a famous name or appear on standard tourist itineraries.
Some are tiny rocky inlets. Others are little stretches of water tucked between cliffs. Depending on the wind and swell, one may be beautifully calm while another is unsuitable for swimming.
These are the types of places that can make a private boat trip feel different from a standard excursion. Rather than following a rigid checklist of attractions, you can adjust the route around:
- Wind direction
- Sea conditions
- Boat traffic
- Crowd levels
- Your group’s swimming ability
- How much time you want to spend at each stop
Local tip: The “best” hidden bay around Comino isn’t necessarily the same one every day. If the wind changes, your skipper may recommend a different side of the island where the water is calmer and more comfortable.
That flexibility is often more valuable than having a fixed list of supposedly secret locations.
When Is the Best Time to Explore Comino’s Quieter Bays?
Timing can make a huge difference to your experience.
The Blue Lagoon is particularly popular during summer, and Malta’s Environmental Health Directorate notes that the area attracts large numbers of visitors, especially during the summer season.
If avoiding crowds is important to you, early morning and later afternoon are generally worth considering.
Early Morning
An early start gives you the best chance of experiencing the coastline before the busiest part of the day.
You can head towards the Blue Lagoon while visitor numbers are still lower, then move on to quieter areas as more boats begin arriving. This approach is particularly useful during July and August.
For a more detailed breakdown of timing, read our guide on the best time to visit the Blue Lagoon in Malta during summer.
Late Afternoon
A later departure can offer another type of experience.
As day-trippers begin leaving, the atmosphere around the coast can become more relaxed. The softer afternoon light also works beautifully against Comino’s limestone cliffs.
If you’re deciding between an early start and an evening experience, our guide comparing Blue Lagoon Malta at sunrise vs sunset can help you decide which suits your plans.
Midday
If midday is the only time that works for your holiday, don’t worry.
You can still enjoy Comino.
The trick is not to spend your entire trip trying to stay in the busiest part of the Blue Lagoon. Swim there, take in the famous scenery, and then move on to other parts of the coastline where the atmosphere may be more relaxed.
Blue Lagoon or the Hidden Bays: Do You Have to Choose?
Not at all.
One of the biggest advantages of exploring Comino by private boat is that you don’t have to choose between seeing the famous attractions and finding quieter places.
You can experience the Blue Lagoon and then continue around the island.
For example, a flexible itinerary might look something like this:
- Start early at the Blue Lagoon.
- Swim and take photographs before the busiest period.
- Continue towards the caves and coastal formations.
- Stop for snorkelling where conditions are suitable.
- Visit a quieter bay or cove.
- Continue towards Crystal Lagoon or Cominotto.
- Spend more time at the places your group enjoys most.
The exact route should always depend on the weather and sea conditions rather than being treated as a fixed schedule.
If you’re travelling with children, the Blue Lagoon can also be particularly appealing because of its shallow water and convenient facilities. Our guide to visiting the Blue Lagoon Malta with kids covers what families should know before going.
What Can You Do Around Comino Besides Swimming?
Comino is much more than a place to jump into the water.
Depending on your interests and the conditions, you can spend your day:
- Snorkelling
- Exploring sea caves
- Taking photographs
- Cruising along the coastline
- Visiting different bays
- Paddleboarding or kayaking
- Relaxing on a beach
- Exploring Cominotto
- Watching the cliffs and rock formations from the water
For a broader list of things to do, our guide to the best summer activities in Comino covers swimming, snorkelling, caves, beaches and other ways to enjoy the island.
One of our favourite things about a private charter is that you don’t have to spend the entire day doing the same activity. You can swim for a while, explore some caves, have a snack, take photographs and then simply cruise along the coast.
Why a Private Boat Is Useful for Exploring Comino’s Hidden Spots
If your main goal is simply to reach the Blue Lagoon, there are several ways to get to Comino.
But if your goal is to explore the coastline, see caves, visit different swimming spots and move away from busy areas when necessary, a private boat gives you considerably more flexibility.
With GOZOblu, your private charter means you can:
- Travel with just your own group
- Choose a route that suits your interests
- Spend longer at the places you enjoy
- Move on when an area becomes busy
- Look for calmer swimming conditions
- Combine Comino and Gozo in one trip
- Enjoy light local snacks and water on board
- Have fuel and port fees included in the price
The route isn’t simply about ticking off attractions. It can be adjusted around the conditions and what your group actually wants to do.
This is particularly useful if you don’t want a rushed excursion where everyone has to leave a swimming stop at the same time.
How to Explore Comino Responsibly
Comino’s natural beauty is exactly why it is important to treat the coastline carefully.
The island and surrounding areas include protected Natura 2000 sites, and the Blue Lagoon, Santa Marija Bay and San Niklaw Bay are among the official bathing areas monitored by Malta’s Environmental Health Directorate.
When exploring the quieter parts of the coastline:
- Don’t leave rubbish behind.
- Avoid damaging rock formations or vegetation.
- Don’t disturb marine life.
- Follow instructions from your skipper.
- Only swim where conditions are suitable.
- Don’t enter caves when sea conditions make them unsafe.
- Be aware of other boats and water users.
A quieter bay isn’t necessarily a safer bay. Some rocky areas have difficult access, strong currents or changing sea conditions, so always follow the advice of your skipper.
The aim is to enjoy Comino while helping preserve what makes it special.
Frequently Asked Questions
There isn’t an official list of “secret bays” around Comino. The phrase generally refers to quieter bays, coves and less-developed sections of coastline away from the busiest Blue Lagoon area. Santa Marija Bay and San Niklaw Bay are two recognised bathing areas, while other smaller coves are unnamed.
Generally, Santa Marija Bay offers a more relaxed atmosphere than the Blue Lagoon, although visitor numbers vary throughout the day and season. Santa Marija Bay is an official bathing area on Comino and forms part of the Natura 2000 area.
Some areas of Comino can be reached on foot, including recognised beaches and bays. However, a boat makes it easier to explore the coastline, view sea caves and reach certain coves and coastal formations from the water.
Early morning is generally the best option if your priority is avoiding the busiest periods. Late afternoon can also offer a more relaxed atmosphere as many day-trippers leave. During July and August, planning your timing carefully is particularly useful.
Crystal Lagoon generally offers a quieter and more natural setting than the Blue Lagoon, although it can still become busy during peak summer periods. It is deeper and particularly popular with snorkellers and confident swimmers.
Yes, but the suitability of a particular swimming stop depends on the conditions and your children’s swimming ability. For younger children, the Blue Lagoon’s shallow water and facilities may be more convenient. A private boat also allows families to adjust the itinerary around comfort and conditions.
Not every cave is suitable for swimming at all times. Conditions, swell, boat traffic, depth and the shape of the cave all need to be considered. Your skipper should advise whether entering or swimming near a particular cave is appropriate on the day.
Yes. A longer private charter can combine Comino and Gozo, allowing you to experience the Blue Lagoon, quieter swimming areas and parts of Gozo’s coastline in one day.
Experience Comino Beyond the Blue Lagoon
The Blue Lagoon may be the reason many people first discover Comino, but it doesn’t have to be the whole experience.
Beyond the famous turquoise water, there are quieter bays, sandy beaches, sea caves, rocky coves, Cominotto and stretches of coastline that are best appreciated from the water.
The real secret is not finding one magical bay that nobody else knows about.
It’s knowing when to move, where to look and how to adapt your route to the conditions.
That’s where a private boat tour in Malta can make such a difference.
With GOZOblu, your day can be built around your group rather than a fixed timetable. You can combine the Blue Lagoon with quieter parts of Comino, spend more time swimming or snorkelling, and even combine Comino and Gozo in a single trip. Fuel and port fees are included, and light local snacks and water are available on board.
If you’re ready to explore Comino beyond the usual tourist route, we’d be happy to help you plan a private day on the water.
Captain Francesco
Professional Skipper & Founder of GOZObluCaptain Francesco is a professional skipper and the founder of GOZOblu. Having spent years navigating the waters around Malta, Gozo, and Comino, he specialises in creating private boat experiences that showcase both the famous highlights and the hidden corners of the Maltese islands.
His local knowledge helps visitors discover quieter swimming spots, scenic coastal locations, and authentic experiences away from the crowds.
