Phytoplankton are microscopic algae that use light and carbon dioxide to make sugar, similar to plants. In the water column, a mix of diatoms, dinoflagellates, and cyanobacteria form the basis of the food web in the estuary and the ocean. In the open ocean with little to no nitrogen, phosphorus and iron, phytoplankton abundances are very low. The coastal waters of the Gulf of Mexico receive runoff from large rivers that increase phytoplankton productivity by providing nitrogen, phosphorus, silicon, and iron. The phytoplankton are grazed on by zooplankton, larval fish and invertebrates and are filtered from the water column by oysters and other bivalves. 

Phytoplankton abundance is measured by fluorescence that is calibrated to a single species culture of microalgae and reported in ug/L. Plots of chlorophyll throughout the study area often show higher concentrations of chlorophyll at locations close to rivers or other sources of nutrient runoff. During the dry season (November-May), the highest chlorophyll will be in the Caloosahatchee, while in the wet season (June-October) the highest chlorophyll will be moved into San Carlos Bay or Pine Island Sound