Mosquito Bay, Vieques, Puerto Rico is considered one of the best bioluminescent bays in the world. However, in January 2014 it went dark and then exhibited low bioluminescence for several months. Read more about this problem in a recent article in the NY Times.
Alarmed that the problem was due to overuse of the bay by tourists, who flock to the island to experience the bioluminescence, the government instituted a partial moratorium on use of the bay, with tours allowed only on the weekends. However, due to a lack of systematic monitoring of environmental quality, there is insufficient information on what factors caused the loss of bioluminescence. Perhaps it was due to overuse of the bay. But another idea is that it was caused by the weather, specifically high winds in January with a shift in wind direction in March caused increased turbidity, turbulence, and loss of dinoflagellates from the bay.