The department of natural resources said on Thursday that the station will help boost conservation efforts for a bay that attracts thousands of tourists a year.
The bay is home to microscopic plankton known as dinoflagellates that emit light through a chemical reaction when disturbed.
The announcement comes amid concerns that the bay's glow has diminished in recent months because of rough seas.
The station will be completed in upcoming months and will measure the water's salinity, oxygen and temperature, among other things.
In 2011 a team with the National Geographic captured the absolute beauty that exists near the Island of Vieques.