This is a really interesting phenomenon way down on the southwest corner of the island. It is a 4 to 6 hour drive from San Juan.
If you go there, there are local companies who take tours. Some are glass bottom boats and others just hoist a pail of water into the boat and stir it.
These bioluminescent creatures/organisims glow when agitated. It has been several years since I was there so you might want to check out what is available. When I lived there it was mostly visited by locals and very few tourists would make the trip down there for that.
I heard something about a story of some astronaut who was guided by this occurence. They are really interesting!