Zooplankton plays a fundamental role in the estuarine food web. Thus, understanding the factors that affect the distribution of estuarine zooplankton is of major concern for the management of estuaries. An integrated modeling approach, coupling a hydrodynamics and an ecological model, is presented here to simulate the three-dimensional dynamics of zooplankton. The hydrodynamics is computed with SELFE, a 3D baroclinic circulation model. The ecological model is based on an extension of EcoSim 2.0, which allows the simulation of several ecological state variables, to account for zooplankton dynamics. Some test cases are presented that validate the changes made in the EcoSim 2.0 and the integration of the hydrodynamic and ecological models. A sensitivity analysis is also performed to check the influence of the input parameters of the ecological model in the final results, showing the phytoplankton's temperature-dependent growth parameters as the most important, for phytoplankton, inorganic nutrients and DIC pools.