This paper presents a differential-difference equations model of a dynamic aquatic ecosystem. This paper departs from other models by considering : (a) specific phyla of phytoplankton, zooplankton and nekton ; (b) their prey—predation relationships ; (c) both allelochemic and antotoxic effects of algae upon zooplankton and other algae ; (d) inter-phyla competition for nutrients. Other factors included are : limiting effects of phosphates, nitrates, silicates, photoperiod, turbidity, temperature, and time lag, as they affect growth and reproduction of the biota. The model uses the western basin of Lake Erie as a test example, but any shallow basin that does not experience thermoclines could be used.