At night in a lagoon fringed with mangrove thickets, kayakers set their paddles down and look to the dark water for a secret of nature seen in few places.

You simply run a hand through the water, and a greenish glow whirls off your fingers like radiant stardust. Many who come here choose to jump out of their kayaks and watch the bioluminescence stream off their hands and forearms as they swim breaststroke.

“Bioluminescence is actually very common, but not in the intensity we find in these ecosystems,” said guide Mark Donaldson, who has been leading groups to the bioluminescent lagoon for eight years.

The mosaic of light underwater, each tiny dot of it resembling a firefly, is produced by microscopic plankton that create light through a chemical reaction when disturbed. The tiny organisms, known as dinoflagellates, feed on blue-green algae that flourish in the salt water lagoon, making their concentrations higher than in regular seawater.

Visitors reach the enclosed lagoon by making a half-hour paddle from a marina in the eastern town of Fajardo through a canal that winds through mangroves. As the sun sets, bats can be seen swooping past overhead.

When first-time visitors emerge in the lagoon and their paddles begin to stir up the glow, some exclaim, “Whoa!” Children point excitedly.

Some people say swimming through it is like sprinkling pixie dust from every inch of the body.

“It was like beads of light that were going off the hairs on your arm,” said Carl Wolf, a lawyer from San Francisco visiting for the first time.

Others call the experience ethereal, ghostly, and peaceful.

When the bioluminescence is brightest, usually from August through October, streaks of light from darting needlefish and stingrays can be seen from the surface. In other months, cooler waters generally decrease the bioluminescence, but it still can be seen.

The effect is particularly striking when there is a new moon or when the moon is obscured below the horizon.

Nevertheless, the glow is nearly impossible to capture in photographs due to the low light.

The lagoon is surrounded by coastal wetlands in the Las Cabezas de San Juan Nature Reserve on Puerto Rico’s northeastern tip and is overlooked by a lighthouse that pulsates from a headland in the distance.

Puerto Rico is uniquely blessed with three bioluminescent lagoons. Tour guides on the outlying island of Vieques claim their spot at Mosquito Bay is probably the brightest in the world. There is another lagoon at La Parguera in southwestern Puerto Rico.

The closest to San Juan and its international airport is Fajardo’s Laguna Grande, or Grand Lagoon.

Interest in the tours has grown in recent years, and on many nights dozens of kayakers squeeze through the canal leading to the lagoon, sometimes colliding with others coming the opposite direction.

Guides pause along the way, explaining the importance of mangroves as nurseries for reef fish and often pointing flashlights into the trees to expose huge iguanas perched on branches.

It is an environmentally sensitive spot, and for that reason nearly all guides choose to lead the trips by kayak rather than motorboat.

Most types of larger boats are prohibited in any case, and kayakers with experience in the lagoons say they believe fuel that leaks from outboard motors harms dinoflagellates and decreases the glow.

Luis Mendez, who grew up near the lagoon and leads kayak tours, said “every night the brightness is different” and that factors such as moonlight, rains, and extended periods of sunshine all have effects.

Regardless, he said most visitors come away pleased, and some say being immersed in that glow was among the best moments of their lives.

IF YOU GO

BIOLUMINESCENT LAGOON TOURS

The tours include all necessary equipment, including life vests and lights to help keep groups together. Microorganisms in the water are harmless, and the lagoon is comfortably warm for swimming at night. Visitors who have taken home a jar of the water have found the glow quickly fades.

Las Tortugas Adventures: 787-725-5169, www.kayak-pr.com; $40 a person for a two-hour tour, including refreshments upon return.

Yokahu Kayaks: 787-604-7375; $35 a person for a tour, including refreshments upon return.

Eco Xcursion Aquatica: 787-888-2887; $45 a person for a tour, including refreshments upon return. Transportation also available from the San Juan area, for $20 extra.