Estuarine hydrodynamics present complex circulation patterns being floods one of the extreme events that needs correct characterization in these environments. In this context, from the point of view of sustainable environmental management and the minimization of associated flood risks in the estuarine banks, numerical models represent highly valuable analysis tools, allowing to develop reliable forecasts. This work presents the results of two numerical models implemented to simulate floods in the river Douro estuary. It is intended to use these models to design and implement an early warning and flood forecast system with capabilities to identify areas that could potentially be inundated. Simulations included several scenarios representing the effect of the current configuration of the sand spit and breakwaters, located at the estuary mouth, in water elevations within the estuary. It was observed that, for floods similar to those that occurred in the past, more serious effects can be expected in the estuarine margins. Results from this study can be used to define adequate solutions to minimize potential economic losses and damage of infrastructures.