Phytoplankton community structure in coastal areas is a result of various environmental factors such as nutrients, light, grazing, temperature, and salinity. The Yucatan Peninsula is a karstic tropical region that is strongly influenced by submerged groundwater discharge (SGD) into the coastal zone. Phytoplankton community structure and its relationship with regional and local water quality variables were studied in four ports of the northwestern Yucatan Peninsula. Water quality was strongly related to SGD, and variations in phytoplankton community structure were related to local nutrient loading and hydrographic conditions, turbulence, and human impacts. Our study provides an ecological baseline for the Yucatan Peninsula and serves as a basis for establishing monitoring programs to predict changes at sites with high hydrological variation and in developing an early alert system for harmful toxic algal blooms.