In Los Tuxtlas, Mexico, there are numerous deep crater lakes in varying trophic states. In a warm eutrophic monomictic lake of the region we analyzed changes in the phytoplankton community and how they relate to water quality. During the periods of circulation, early and late stratification, there was an increase in species diversity marked by an increase in the abundance of many species of diatoms and chlorophytes. These periods were characterized by low transparency, high specific conductance, and high concentrations of ammonium and dissolved silica. Microcystis aeruginosa dominated during the entire stratification period, when both diversity and succession rates were low. Stratification was characterized by high temperatures (> 30 °C), low transparency, high pH, and high concentrations of soluble reactive phosphorus and nitrate. Thus, in Lake Chalchoapan, physical changes associated with stratification, circulation, and tropical seasonality determine the succession dynamics of the phytoplankton community.