The present research is concerned with some numerical developments and practical application of a physically based numerical model FreshWaterSheds that incorporates a finite element solution to the steady/transient problems of the joint ground/surface fresh/salt water flows in inland and coastal regulated watersheds. The proposed model considers surface and groundwater interactions to be 2-D horizontally distributed and depth-averaged through a diffusive wave approach. Infiltration rates, overland flows and evapotranspiration processes are considered by diffuse discharge from surface water, unsaturated subsoil and groundwater table. New improvements also allow for the management of surface water flow control through the capacity of diversion on flooding zones of catchment areas, as well as on river beds, spillways and outflow operations of floodgates in weirs and dams of reservoirs. Practical application regards the flooding hazard of Aznalcóllar toxic spillages. This flooding disaster was caused by the sequential ruptures of the dikes of two mining residual reservoirs of a pyrite mine, releasing about 10•10 6 m 3 of contaminated wastewater and mining sludge onto the Guadiamar River. The numerical model was adapted to the wastewater and sludge properties of both sudden spillages, as well as to the river bed, the flooded zones and the underneath alluvial aquifer. The model simulation and calibration were made during the date of this hydrological hazard to the likely discharges and dual hydrograph produced by the sudden twofold failure of both reservoirs.