The History of Puerto Rico’s Bioluminescent Bays

It is a fact that people were living beside these waters long before the Taíno, and long before Spain. In 1991, archaeologists Luis Chanlatte Baik and Yvonne Narganes of the University of Puerto Rico uncovered a human skeleton at Puerto Ferro in Vieques, a short walk from Mosquito Bay. The remains are roughly four thousand years old. He is the oldest documented human being ever found in Puerto Rico, he was found beside a bioluminescent bay, and he predates the Taíno by millennia.

And on the shore of the bay at La Parguera itself, between the village and Montalva, there is a site the Historic Preservation Office carries on its register as Papayos, fifty feet from Papayo Bay, exactly where the Papayo community sits today. Irving Rouse described it in 1937: eighteen shell middens, none of them with pottery. He excavated one and found shell, charcoal, ash, and crude stone and shell tools, and concluded that the absence of ceramics placed it in Period I, the preceramic era, before the pottery-making peoples reached this island, older than the Taíno by a wide margin.

Archaeologists returned in 1979 and again in 1990 and reached the same conclusion.

Rouse did not invent the name. He took it from the settlement that was already standing there, Papayos, the community on that shore. It is still standing. There are houses fifty feet from the water. The eighteen middens, the village Rouse walked through in 1937, and the porch lights you can see from a boat tonight are all the same piece of ground.

So the settlement is Papayo, the bay is Papayo Bay, and Papayo is a Taíno word, and anyone living there will tell you the name of their community comes from the Taíno who lived on that shore. Shell heap, village, and water have carried one name the whole way through. The people changed. The address and the name never did.

So: continuous human presence, for thousands of years, beside two of the three glowing waters. That much is not a theory. Those are facts, established by archaeological excavation and empirical evidence.

Atabey, and what water meant

The Taíno were a deeply spiritual people, and among their deities was Atabey, also written Atabei, Attabeira, Atebeyra. She was the ancestral mother of everything they knew. Her realm was water: not only rivers and rain, as she is often reduced to, but lakes, streams, the sea itself, and the movement of the tides. Her worship extended across Cuba, Hispaniola, Borikén, Jamaica, and into the Lesser Antilles. She was also the mother of Yúcahu, the highest spirit in the Taíno order. After the conquest she was folded into the Virgin Mary, which is how a great deal of her survived at all.

That is the frame our ancestors already carried. Every body of still water was already hers.

Everything above this line is documented. What follows is mine.

What I believe happened here

The chroniclers left no record of what the Taíno did in these particular waters. I have looked, in Pané, who wrote the first account of Taíno belief around 1498; in the modern scholarship on cacíques and cemíes; in the Park Service and Smithsonian material on ceremony and healing. None of them place a ritual in a glowing bay. That absence is real, and I am not going to paper over it.

But they did leave the pieces, and I have spent almost thirty years setting them beside each other.

Consider what these people already believed. All still water belonged to the mother of the highest spirit they knew. They carried the sick to the water, to Atabey, to be purified. And in all of their territory there was exactly one water that answered back, that lit under a hand, under a paddle, under a body wading in at night.

If they worshipped the waters as Atabey’s realm, if they had a settlement at Papayo, and if their principal cacíque had his village less than ten miles away, then it is not possible that they did not know about the glowing water in their own back yard.

A people who believed the first two things could not have overlooked the third. That is not faith on my part. That is a culture behaving consistently with itself.

Legends and folk tales are not part of the bibliography I have assembled in my research. But the ones I have gathered, both from speaking with Taíno descendants and from the tales carried by the storytellers of an earlier generation, all revolve around the same idea: that the Taíno brought people here, the sick, the cacíques, warriors and behiques, and put them in the water. And what I find in them is that the bath was a judgment, not a cure. Survive, and Atabey had returned you because something was left unfinished. Do not survive, and she had accepted you, because you were worthy and fit to cross over to the ancestors. Either way, her judgment was final and never questioned. That is how deep their faith ran.

There is one water in their world that answers when you touch it.

And then a Spaniard heard about it

The conqueror of Puerto Rico, and also our first governor, was Juan Ponce de León. Before coming to our island he was in Hispaniola, and governed at Santo Domingo, another island, but inhabited by the same Taíno who lived in Borikén. In his years there he learned some of that language and could speak it partially. Enough to ask about certain things and understand the basics. Not enough to understand everything correctly.

That is how he knew, before he ever arrived, that the principal cacíque of this island lived to the south, on a bay, and it is why he came in through that area to meet him and negotiate a truce, to avoid confrontation. That was the plan. But when he met Agüeybaná he came face to face with the spirituality of our ancestors, and he agreed to perform the guaitiao with him: the most profound Taíno rite, in which two men exchange names and become one another’s kin.

Now put a man beside them who understands about half the words.

Once Ponce de León performed the guaitiao he was immediately accepted by the Taíno. If the principal cacíque had exchanged names with him, he carried that cacíque’s blessing, and that was not something taken lightly. He was now Agüeybaná, and Agüeybaná was now Juan Ponce de León.

After that, all of the Taíno’s knowledge was at his disposal, but not everything he was told was fully understood.

Now think about it for a second. Sacred water. The sick, carried in. Bodies going under at night. Bodies coming back out alive. Assemble those four fragments with half a vocabulary and a European head, and you do not get a Taíno judgment rite. You get something much simpler and much more seductive.

A water you enter, and do not die.

This is my hypothesis, and I offer it as one: a reading that blends Taíno legend, the documented record, and plain common sense. Because how is it that after his time in Puerto Rico, once he was removed from the governorship, he spent the rest of his life searching for a place where a man could enter the water and stay young forever? No Taíno ever spoke of anything like that. What we have is Atabey, the ritual in the water, the principal cacíque living beside the bay, and a settlement on the shore where the water glows.

Ponce de León died in Florida of a wound taken in that search. But having gone over his entire documented movement through the Caribbean, the bioluminescent bay is the only place I can point to that matches the description of what he was looking for. And he did not merely stand beside it, he performed the guaitiao there.

Three readings of one water

What makes this history worth telling is that the same phenomenon was read three completely different ways by three groups of people who all stood on the same shore.

The Taíno brought the frame of Atabey, and read the light in the water as the mother goddess answering them from within her own realm.

The Spanish brought sixteenth-century Catholicism, and read it as witchcraft, and I can only think they concluded witchcraft because they saw that the Taíno revered those waters. On Vieques the legend says exactly that: that the Spanish feared the glowing water as bewitched, and that stones were sunk at the mouth of the bay to choke it off. Even the name of the pirate Roberto Cofresí is often attached to that stonework, and it is documented that he kept a hideout on Vieques. I have found no document showing that he dropped those stones, but people in Vieques still tell the story. So even though I find it plausible, it stays where it belongs: a legend, told as legend.

The reading of why is mine, and it runs in two directions at once. A sixteenth-century sailor who puts an oar into black water and watches the water light itself does not need to witness a ceremony he has only heard about in order to arrive at the devil, he arrives there on his own, with what he brought from home. And a pirate three hundred years later has a reason that owes nothing to superstition: a glowing wake shows anyone watching exactly where you went and exactly when. Fear and operation point at the same stones.

And Ponce de León read it as a promise, and went looking for the wrong thing for the rest of his life.

What we know today as La Parguera was established as a fishing village in 1825. It predates Lajas itself, which was constituted as a municipality on July 1, 1883, separated from San Germán, with 6,238 residents. The new municipality was organized into eleven barrios, and La Parguera was one of them from the first day. So it is a fact that the community on that bay already existed, and already had its own name, before the town around it was official.

You will read almost everywhere that the bay was discovered in 1938, when fishermen noticed their nets glowing as they hauled them out. Treat that gently. A local fisherman does not discover, in 1938, a water that had been lighting up on that shore for centuries, and the barrio was not only on the map with its own name fifty-five years earlier, it is home to Papayo, which the Taíno were already calling by that name.

1950: the first boat

The first commercial visits to a bioluminescent bay in Puerto Rico begin here. In 1950, Fondo de Cristal introduced the first glass-bottom boat on the bay at La Parguera. Everything that exists today, every kayak outfitter, every catamaran, every pontoon on three bays, descends from that boat.

It is not running. The vessel has been out of service for years, awaiting a Coast Guard re-inspection the family operation cannot afford to prepare it for. Seventy-six years after it opened this industry, the boat that started it is tied up.

1960: the world finds out

It was not until July 1960 that National Geographic published an article by Paul A. Zahl, a Harvard-trained biologist who served as the Society’s senior scientist from 1958 to 1975 and published more than fifty articles for the magazine. He came, he visited the bay, and he left so struck by it that he called the piece “Sailing a Sea of Fire.” That is the moment this bay stopped being a local fact and became a destination. Puerto Rico’s own tourism magazine followed with its own article the next year.

But the science had arrived just ahead of it. In 1957, Ramón Margalef, one of the most important ecologists of the twentieth century, published on the phytoplankton of these coasts, and again in 1961 on the hydrography of this southern coastal area. Through the 1960s and 1970s, Howard Seliger and William McElroy of Johns Hopkins built the ecosystem model for how these blooms accumulate, and the bay they built it on was this one. La Parguera had become the world’s scientific reference for the entire marine bioluminescence phenomenon.

The houses on the water

Anyone who has been to La Parguera has seen them: the casetas on stilts and the floating houses tied along the mangrove. Their legal status is genuinely complicated, a federal court in 1993 described many of the older structures as “grandfathered” by the sheer number of years since they were built, while the agencies maintain that the structures sit on public water without valid permits. Both of those things are in the record. What is not complicated is why the government came after them in the first place. It was never architecture. It was sewage.

These structures sat over the water with nothing to connect to. By 1968 the EPA had documented roughly 120 of them discharging untreated waste straight into the mangrove and the sea. In November 1969 the Public Service Commission ordered the owners to remove the structures within sixty days on three grounds: clandestine construction, occupation of navigable waters without permits, and pollution. What followed came out of that. In 1970 came the removal order against some 121 houses. In 1976 came the Supreme Court ruling that struck it down on jurisdiction rather than on the merits. On July 9, 1977 came the cutoff for new construction, and in 1978 an agreement was reached with the U.S. Army Corps of Engineers.

But the thing that actually fixed the water was plumbing, not litigation. PRASA, Puerto Rico’s water utility, proposed a treatment plant and sewer system in 1973. After a decade of failures, including a bankrupt contractor and a defective gravity main, the EPA and PRASA set a hard date to have the system running: July 31, 1985. A federal discharge permit took effect that October requiring zero untreated sanitary discharge into the bay, and the casetas had ninety days to connect to the trunk line or install approved treatment of their own. The owners themselves paid for much of it, their spokesman put the figure near half a million dollars, and said it allowed other households in the community to connect as well.

That fixed the problem. It ended the direct discharge of raw sewage from the casetas into the bay, and that was the single largest source of contamination. No system is perfect, and like any other oceanfront community in Puerto Rico there are still instances when it fails, pump failures, overflow in heavy rain events, and runoff from land that has nothing to do with the houses.

Still, it is worth saying plainly, because almost nobody says it: the worst thing that was happening to this bay was stopped, and the people who lived over the water helped pay to stop it.

Missing from the town’s own history

Papayo Bay sits within the municipality of Lajas, and Lajas has an official published history, part of the state government’s series documenting each municipality. It covers the founding, the mayors, the parish, the barrios. But it does not mention the bioluminescent bay. Not once.

When I first noticed that, I assumed it was carelessness. But researching it, I found that those volumes are written out of the municipal archive, founding papers, censuses, administration, and Papayo Bay never generated administrative paper. It was known by the people, and it was known for its glowing water, but that leaves no file and no paper trail. The most studied bioluminescent bay on earth, the scientific model for the whole phenomenon, and its own town’s official history has nothing to say about it.

And that is the whole point of this page: to tell the history that was never written, only told.

Mosquito Bay is a different story. The Spanish never permanently settled Vieques in the early centuries, and for roughly three hundred years it was effectively lawless ground, worked by pirates, smugglers and rival European powers. Permanent Spanish settlement only begins in 1811, and the municipality is formally constituted in 1875.

Mosquito Bay sits on the south coast of that small island, between the Puerto Ferro and Puerto Real barrios, less than a mile from Esperanza. Local legend traces its name to Cofresí’s sloop El Mosquito, and it makes for a good story, but I believe the direction is backwards.

Cofresí named the boat, and the legend says he named it that way because it would sting and be gone, like the insect. And since his boat was El Mosquito and he operated out of that area, the bay is said to have been named for it. But as a historian I have to follow the evidence in front of me, and the Vieques coast carries a whole series of chart names laid down in one sweep by navigators, Mosquito, Puerto Ferro, Puerto Real, Puerto Diablo. Mosquito belongs to that series, and that series predates Cofresí. So most likely it was the bay that named the boat.

The Navy years

Mosquito Bay sits in a strip of land between the eastern and western ends of Vieques, which the U.S. Navy held for more than sixty years. That fact alone debunks a story people tell on the main island, and that some tour sellers repeat: that the bay was inside the live impact area and sealed off. It was not. It sat in the civilian strip in the middle, where people lived. The misconception comes from something real, the Navy did hold the surrounding land out of development, which meant no subdivisions, no lighting, no runoff. The protection was a side effect of occupation, a buffer zone around military exercises, not a prohibition on entry.

The Navy left in 2003 after years of protest, and the former range became a National Wildlife Refuge.

Recognition

In 1980 the National Park Service designated Puerto Mosquito a National Natural Landmark. On June 1, 1989 it became a Natural Reserve under Puerto Rico law, covering some 9.8 square kilometers. In 1999 Congress directed the Secretary of the Interior to study the bay for possible inclusion in the National Park System, which never happened. In 2006 Guinness World Records recognized it as the brightest bioluminescent bay in the world. And it was not until 2012 that the Puerto Rico Planning Board approved a management plan for the reserve, twenty-three years after the designation itself.

The reserve is co-managed today by the Department of Natural and Environmental Resources and the Vieques Conservation and Historical Trust, with active mangrove, seagrass and coral restoration funded through NOAA. Combustion engines are prohibited. Swimming is not permitted.

Our last bioluminescent bay is not really a bay at all. Laguna Grande is a saltwater lagoon of roughly fifty hectares, joined to the sea by a long narrow channel through red mangrove, and you reach the open water by paddling that tunnel in the dark. It sits inside the Las Cabezas de San Juan reserve, alongside the nineteenth-century Spanish lighthouse.

A 2013 paleoenvironmental study reconstructing 3,600 years of this site made a surprising discovery: the modern lagoon formed roughly 575 years ago, and its high dinoflagellate densities appear relatively recent, within the last two centuries or so.

That finding is exciting, because it opens the door not only to new areas developing in the future, but to the possibility that some are forming right now.

The Puerto Rico Conservation Trust acquired the headland in 1975, and it was designated a Natural Reserve in 1986. Swimming is not permitted, entry requires an authorized operator, and the tours are almost entirely by kayak, a completely different model from the boat that opened La Parguera in 1950.

What you read here today may not be what you read next month, because I keep a working bibliography of just over two hundred sources on these three waters, scientific papers, theses, federal and Commonwealth files, press, and tourism material. A large share of it is open and readable, and that is what I have used to build this website. A meaningful share is not. Those documents sit in the National Archives, in Park Service and Planning Board files, in the Archivo General de Puerto Rico, and in the libraries of the University of Puerto Rico, and they have to be pulled by hand.

Anything on this website that comes from a document I have not personally read, I will say so. And it will keep evolving as I am able to reach them.