► We developed an integrated and lumped surface/groundwater numerical model. ► We developed and applied a new approach for actual evapotranspiration processes. ► We applied novel approaches for infiltration rates and overland flows processes. ► Interface and GIS developments manage simulated conditions and numerical results. ► Application allows mass conservation on deep water bodies with complex hydrogeology. This research and practical application is concerned with the development of a physically-based numerical model that incorporates new approaches for a finite element solution to the steady/transient problems of the joint surface/groundwater flows of a particular region with the help of a Geographic Information Systems to store, represent, manage and take decisions on all the simulated conditions. The proposed surface–subsurface model considers surface and groundwater interactions to be depth-averaged through a novel interpretation of a linear river flood routing method. Infiltration rates and overland flows generation processes are assessed by a sub-model which accounts for this kind of surface–groundwater interactions. Surface–groundwater interactions consider also novel evaporation and evapotranspiration processes as a diffuse discharge from surface water, non-saturated subsoil and groundwater table. The practical application regards the present flooding of the Meirama open pit, a quite deep coal mining excavation, with freshwater coming from the upper Meirama sub-basin, in the context of the water resources fate and use at the Barcés river catchment (∼87.9 km 2 ), Coruña, Spain. The developed model MELEF was applied to the complex geology of a pull-apart type sedimentary tertiary valley and the whole of the water resources of the Barcés River drainage basin, down to its outlet at the Cecebre Reservoir. Firstly, the model was adapted and calibrated during a simulation period of three and a half years (2006/2009) with the aid of the historically registered hydrological parameters and data. Secondly, the results predict the most likely forthcoming evolution of the present flooding of the Meirama open pit to reach therein a total depth level of almost 200 m, as regards the projected evolution of the water resources, climatology and usages.