What is chlorophyll-a?  
Chlorophyll is a green pigment in plants that turns light energy into food and allows plants to grow, and releases oxygen in a process called photosynthesis. The microscopic one-celled plants that float in healthy waters are called phytoplankton. By measuring the amount of chlorophyll in the water, scientists can determine the density of phytoplankton in an estuary, and the amount of primary productivity (the conversion of light energy into plant material) taking place as well.
Why do Gulf River students measure chlorophyll-a? 
Phytoplankton forms the base of the aquatic food web in an estuary. It is eaten by zooplankton (microscopic animals) and small fish, which, in turn, are eaten by larger creatures. The abundance of healthy animals in an estuary often depends on the amount of phytoplankton and primary productivity taking place. NOAA Ocean Service Education