This study constructed a System Dynamics model to investigate primary production and nutrient dynamics in aquatic ecosystems under two types of nutrient-limiting mechanisms: intracellular VS. extracellular nutrient limitation. Different trophic states: oligo-trophic and trophic, are designed to test the responses of primary production and inorganic nutrient behavior. Simulation runs show that, when external inorganic nutrient concentrations are low, the behavior of primary production and inorganic nutrient dynamics from both nutrient-limiting mechanisms is significantly different. Internal nutrient-limiting mechanism could produce higher primary production rate and biomass accumulation. As external nutrient concentrations increase, the difference is reduced When external nutrient concentrations are high, the difference will be minimized The study concludes that external nutrient-limiting mechanism may be applied to trophic or polytrophic aquatic systems, while internal nutrient-limiting mechanism can be employed for either oligotrophic or trophic aquatic system.