A mathematical model for computer simulation of aquatic ecosystems was developed and adapted to lake and estuarial systems. The model is capable of simulating the annual cycle of ecologic successions involving algae, bacteria, zooplankton, fish and benthic animals and the interdependent relationships between biota and abiotic substances carried in the natural aquatic system. It is water quality oriented, predicting the temporal and spatial distributions of temperature, dissolved oxygen, biochemical oxygen demand, pH, conservative constituents (e.g., salinity, TDS, etc.), toxicity, nitrogen (three forms), carbon dioxide, and phosphorus as well as the biomass of each trophic level in the system. The basic formulations in the model are based on kinetic principles and the law of Conservation of Mass. Algal growth kinetics are governed by a Michaelis-Menton relationship including light, temperature, carbon, nitrogen and phosphorus.