How Mayotte’s Lagoon Was Formed — Between Volcano, Coral and Currents

The buoys drift away, the lagoon opens.
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The engine barely hums before the shoreline slips behind us. On board, the air still carries the weight of heat, but ahead, the horizon turns liquid, almost unreal. I’m with Seablue Safari, guided by Mathias, a pilot who knows these waters the way one knows a familiar path. We’ve barely left the coast when he begins to explain.​

Here, nothing is accidental. Mayotte’s lagoon is not simply a sheltered body of water. It is a slow construction, born from fire, shaped by coral, and carved by currents.

To understand it, you have to go back long before the mantas, long before the dolphins — back to the very origin of the island. A landscape that began forming millions of years ago, with its present contours gradually taking shape around 3 to 4 million years ago.

Origins: an island born from fire

Long before it became a lagoon, Mayotte was a volcano.

Located in the Comoros archipelago, the island formed through volcanic activity estimated between 8 and 10 million years ago. Like many tropical islands, it was later colonized by corals — organisms capable of building, generation after generation, vast living structures.

Around the island, corals progressively formed a barrier reef. Then, slowly, almost imperceptibly, the volcanic mass began to subside. The corals, however, continued to grow upward toward the light, maintaining their position near the surface.

This mechanism — first described in the 19th century by Charles Darwin — explains the formation of tropical lagoons: a sinking island, a rising reef, and between them, a protected body of water.

In Mayotte, this process created one of the largest enclosed lagoons in the world.

A lagoon is not a lake

At first glance, the lagoon may appear calm, almost still. But that impression is deceptive.
A lagoon is a living system, constantly in motion.
Protected by a barrier reef, it remains connected to the open ocean through openings known as passes.

These passes allow:

• water renewal
• nutrient exchange
• circulation of larvae and marine life

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Without them, the lagoon would stagnate. With them, it breathes.

The S Pass — a defining feature of Mayotte​

Among these openings, some have become iconic. One of them is the famous S Pass.
From above, it traces a sinuous curve through the reef barrier. Below the surface, it acts as a channel where water masses rush in, accelerate, slow down, and mix.

Its shape is no accident.

While currents and erosion play a major role in carving the pass, its trajectory may also be influenced by an older structure. During periods when sea levels were lower, parts of what is now submerged were exposed, shaped by relief and freshwater flows.

An ancient valley, gradually flooded as sea levels rose, may have guided the formation of this channel.

Since then, ocean currents have taken over, widening, sculpting, and maintaining this passage, which has become essential to the lagoon’s circulation.

These areas concentrate life: fish, predators, plankton. They are corridors of movement — but also zones of encounter.

How passes are formed
Passes are not simple gaps in the reef. They are zones where energy concentrates.
They form where:

• waves strike with the greatest force
• currents find a point of entry
• extreme events, such as cyclones, weaken the structure

In Mayotte, some passes may also follow older geological features inherited from the island’s volcanic past.
Over time, these zones widen, deepen, and become permanent channels.

A volcano still active beneath the sea

But Mayotte’s geological story does not end there.

In 2018, a new underwater volcano was discovered several dozen kilometers east of the island, at a depth of more than 3,000 meters. A recent formation, born from intense activity, reminding us that the region remains geologically active. This volcano did not shape the present lagoon — it is far too recent — but it highlights an essential reality:
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Mayotte is not a static landscape. It is a territory still in motion.

A fragile balance

Today, Mayotte’s lagoon is an exceptional ecosystem. Seagrass beds, coral reefs, sandy areas and passes form a complex network where each element plays a role.

But this balance is fragile. Human pressure, pollution, overfishing, and climate change all have the potential to disrupt exchanges, alter balances, and weaken the system.

Passes, in particular, are critical zones. They concentrate life — but also impact.

Between story and reality

The engine cuts. Silence settles.

Around us, the lagoon appears still, almost frozen. This is where Mathias chose to tell his story. Not the one about mantas or dolphins, but the deeper one — of a landscape shaped over millions of years.

He speaks of another feature of Mayotte’s lagoon: its double barrier reef, a rare structure on a global scale, parts of which have collapsed over time, revealing a system as complex as it is fragile.

In recent years, political ambition has grown: to have the lagoon recognized as a UNESCO World Heritage Site. On paper, such recognition could offer additional protection to this unique ecosystem.

But for Mathias, who has navigated these waters for more than thirty years, reality is more nuanced.

Over time, he has watched the lagoon change.
 Construction spreading.
Waste accumulating.
Wastewater finding its way into the sea.
And more recently, additional human impacts placing further pressure on an already fragile system.

Without raising his voice, he speaks of a gap. Between announcements and reality. Between image and ground truth.

In this context, some see a strong signal. He sees a risk: that recognition becomes a showcase, without always being matched by the means needed to protect what it claims to preserve.

The engine starts again, softly.

The boat glides over water of unreal clarity. Around us, the lagoon remains what it has always been: a space of life, balance, and raw beauty.

So Mathias takes us further. To observe. To understand. To experience.​

While it is still possible. Because some wonders are not meant to be admired. They are meant to be protected.

​The engine starts again, softly.

The boat glides over water of unreal clarity. Around us, the lagoon remains what it has always been: a space of life, balance, and raw beauty.

So Mathias takes us further. To observe. To understand. To experience.​

While it is still possible. Because some wonders are not meant to be admired. They are meant to be protected.

Mayotte Lagoon: Key Facts

Is Mayotte one of the largest lagoons in the world?

Yes. Mayotte is widely described as one of the largest enclosed coral lagoons in the world, with estimates often ranging from more than 1,000 km² to around 1,500 km² depending on the source and measurement method. Its reef system is also remarkable because it includes a rare double barrier reef.

What are some of the world’s largest lagoon systems?

The world’s largest lagoon systems include New Caledonia’s lagoon, Lagoa dos Patos in Brazil, Mar Menor in Spain, Laguna Madre in Mexico and the United States, and Mayotte’s enclosed coral lagoon. These systems are difficult to rank precisely because some are coastal lagoons, others are coral reef lagoons, and their measured surface areas vary by definition.

Why is Mayotte’s lagoon so deep?

Mayotte’s lagoon is unusually deep because it formed around an ancient volcanic island that gradually subsided while coral reefs continued to grow upward toward the light. This long geological process created a wide and deep protected lagoon between the island and the outer reef barrier.

Why are reef passes important in Mayotte?

Reef passes are essential because they connect the lagoon to the open ocean. They allow water renewal, nutrient exchange, larval dispersal, and the movement of marine life. In Mayotte, passes such as the S Pass are also biodiversity hotspots where currents concentrate life.

What makes Mayotte’s lagoon fragile?

Mayotte’s lagoon is vulnerable because its ecological balance depends on water quality, healthy coral reefs, seagrass beds, and functioning reef passes. Pollution, wastewater, plastic waste, coastal construction, overfishing, climate change, and extreme weather events can all weaken this balance.