Abstract Degradation of litter from mangrove forests adjacent to the creeks at Sagar Island of the Hooghly–Matla estuarine ecosystem is one of the principal sources of nutrient to the estuary. Nutrients augment the growth of phytoplankton, which in turn stimulates the production of zooplankton. Zooplankton serves as major food source for fish population of this estuarine system. Here, a dynamic model with three state variables (nutrient, phytoplankton, and zooplankton) is proposed using nitrogen (mgN/l) as currency. Input of dissolved inorganic nitrogen as nutrient, water temperature, surface solar irradiance, and salinity of upstream and downstream of the estuary, collected from the field, are incorporated as graph time functions in the model. Calibration and validation are performed by using collected data of two consecutive years. Model results indicate that the growth of zooplankton and phytoplankton are enhanced by increase in nutrient input in the system. Zooplankton biomass is affected by decrease in the salinity of the estuary. Sensitivity analysis results at ±10% indicate that maximum growth rate of phytoplankton (Pmax) is the most sensitive parameter to the nutrient pool although growth rate of zooplankton (gz) and half saturation constant for phytoplankton grazing by zooplankton (Kz) are most sensitive parameters to phytoplankton and zooplankton compartments, respectively. The model depicts the present status of plankton dynamics, which serve as major food resource for herbivorous and carnivorous fish species of the estuary. Effect of deforestation is tested in the model. Therefore, from management perspective, this model can be used to predict the impact of mangroves on nutrient and plankton dynamics, which will give complete information of both shell and fin fish productions in the estuary.