In this study, eutrophication was investigated in Lake Ontario to identify the interactions among effective drivers. The complexity of such phenomenon was modeled using a system dynamics approach based on a consideration of constant and variable stoichiometric ratios. The system dynamics approach is a powerful tool for developing object-oriented models to simulate complex phenomena that involve feedback effects. Utilizing stoichiometric ratios is a method for converting the concentrations of state variables. During the physical segmentation of the model, Lake Ontario was divided into two layers, i.e., the epilimnion and hypolimnion, and differential equations were developed for each layer. The model structure included 16 state variables related to phytoplankton, herbivorous zooplankton, carnivorous zooplankton, ammonium, nitrate, dissolved phosphorus, and particulate and dissolved carbon in the epilimnion and hypolimnion during a time horizon of one year. The results of several tests to verify the model, close to 1 Nash-Sutcliff coefficient (0.98), the data correlation coefficient (0.98), and lower standard errors (0.96), have indicated well-suited model’s efficiency. The results revealed that there were significant differences in the concentrations of the state variables in constant and variable stoichiometry simulations. Consequently, the consideration of variable stoichiometric ratios in algae and nutrient concentration simulations may be applied in future modeling studies to enhance the accuracy of the results and reduce the likelihood of inefficient control policies.