Since Water Policies around the world establish the need to manage the aquatic systems through the use of water bodies, a hydromorphological descriptor such as the flushing time may be utilized as a good homogeneity and water quality criterion to distinguish between different types of water bodies. In order to achieve this task, a methodological procedure has been proposed involving a hydrodynamic forcing analysis, an approach to calculate flushing time and a sensitivity analysis of the results applied to the Suances Estuary. This method allows taking into account the different spatial regions on an estuary and the temporal variations of the main forcing. Consequently, the role of bathymetry, freshwater river inflows and oceanic tides on the flushing time is investigated using a two-dimensional numerical model. The hydrodynamic module integrates the depth-averaged mass and momentum equations in the time and space domains as well the transport module solves the depth-averaged advection-diffusion equation. Both modules were calibrated and validated using field data collected during spring and neap tidal cycles. Water levels and current velocities were used in the hydrodynamic module while salinities were compared in the transport module. In order to characterize the spatial variation in water renewal conditions, several boxes were selected along the estuary to evaluate the flushing time. The mass reduction is monitored in time and the flushing time at each part of the estuary was computed for several scenarios and analyzed with a multi-sensitivity analysis.Most of the river estuary basins in Northern Spain are characterized by their small surface area, short length and steepness, leading to a rapid hydrological response to rainfall and, consequently, a high variability in the river flow. During extensive dry periods during which the river flow is very small, pollutants could remain for long periods in the estuary posing an environmental risk.