The two-dimensional barotropic, hydrodynamic and transport model MOHID is applied to the Patos Lagoon system using a nested modelling approach to reproduce both the lagoon and estuary hydrodynamics. A new Lagrangian oil spill model is presented and used to simulate a hypothetical oil spill in the estuary. Hydrodynamic fields are validated and used to force the oil model. Results show that the hydrodynamics of this system is mainly controlled by the wind and freshwater discharge. The dispersion, concentration and thickness evolution of the oil in the first day after the spill is determined by the equilibrium between these two factors. The freshwater discharge is the major factor controlling the oil dispersion for discharges greater than 5000 m3 while the wind assumes control for lower discharge amounts. The results presented are a first step toward a coastal management tool for the Patos Lagoon.