Two-dimensional depth-averaged water quality models are useful tools to evaluate the environmental status of non-stratified shallow estuaries. Sensitivity analysis can be used in order to investigate the robustness of model predictions, as well as to identify the most important parameters for model calibration, providing information about the factors that mostly contribute to the output variability. This paper presents the application of a 2D water quality model to a shallow estuary. The model was developed by the authors and solves the mass transport equations for the Escherichia Coli concentration, including the effects of water temperature, salinity, solar radiation and turbulent diffusion. The sensitivity of the concentration of Escherichia Coli in the estuary to input data is analyzed, and the most sensitive parameters are identified in order to aid modellers in the calibration process, in the definition of model output uncertainties, and in the interpretation of the numerical results.