The lagoon draws hundreds of tourists a year who rent kayaks or boats by night from the nearby city of Fajardo to observe the water emit a greenish light when fish swim by or when they trail an arm through it.
Scientists and residents were concerned that the lagoon stopped glowing because of runoff from the construction of a nearby water and sewer treatment plant, or because of people cutting down mangroves to allow larger boats into the area.
Scientists celebrated that it wasn't a man-made problem, but their investigation also found that the lagoon has high amounts of fecal matter and other bacteria.
Those findings demonstrate a need for the water and sewer treatment plant currently being built, said Laura Velez, president of the Environmental Quality Board, which monitors such projects.
Government officials said the contamination problem was the result of a nearby community lacking a proper sewage system.
Residents had asked that the plant be moved elsewhere when the lagoon began going dark, and the government temporarily suspended construction of it for two weeks to allow scientists to investigate.
Alberto Lazaro, president of the state Water and Sewer Authority, said the agency is contemplating relocating the plant and that officials will meet with residents before choosing a location.