THE BLACK WATER IS AMAZING , but below the surface, there is evidence of magic. Run your finger over it and it will come to life, sparkling like blue stars. Raise your hand and it will sparkle: They say humans are made of stardust and that may be true here. Above, the moon is hidden behind the clouds, but it’s better this way: a beam of light from above will only spoil the luminous effect.

This is what it feels like to glide through a bioluminescent bay: a rare ecosystem that occurs when microscopic organisms called dinoflagellates converge in numbers of thousands per gallon. When agitated, they glow in the dark, turning a tropical night into something out of a science fiction movie.

These sparkling ecosystems occur in only a handful of locations around the world, usually in warm waters with narrow access to the open sea.

One is the famous emerald waters of Ha Long Bay in Vietnam, which was declared a UNESCO World Heritage Site in 1994. Another is Luminous Lagoon , in the Jamaican wetlands.

The first of the three bioluminescent bays is Mosquito Bay located on Vieques, a small island seven miles off the southeast coast of the main island. This is the most sought after bioluminescent bay experience because it is traditionally the brightest of the bunch ( declared so by the Guinness Book of World Records in 2006). Visiting the Vieques area often requires an overnight stay because the ferries stop running early in the evening.

Near the town of Fajardo on the northeastern tip of the main island, a visit to Laguna Grande allows you to pass through mangroves, partly protected by the coral reef of the Cabezas de San Juan reserve. And finally, there’s La Parguera in the southwestern town of Lajas , a little over two hours’ drive from San Juan. The area remains largely untapped by tourism, which means its quiet natural wonders and abundant wildlife are largely undisturbed.