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TOUGH2 is an integral finite differences numerical simulator for non-isothermal multiphase flow in fractured porous media, which can manage complex spatial discretizations. Numerical simulation accuracy is affected, among other things, by grid resolution. Increasing the grid resolution requires computational and operating costs depending on the number of nodes and variables processed. The complexity of the management of the model increases when unstructured grids and local refinement are used. In order to improve the management and optimize the activities to update the model, an open source pre-processor has been developed using the open source codes GRASS GIS, SQLite and AMESH. Operations such as domain discretization, rock type assignment and mesh file generation have been automatized. Graphical interfaces allow for a user-friendly utilization. Operating errors and time required by pre-processing activities to generate and update locally refined unstructured grids have been reduced. Productivity in numerical modeling has been substantially increased. A novel approach to generate TOUGH2 input file through GIS is presented.TOUGH2GIS automatically creates locally refined unstructured 3D grids.Rock types attribution to grid blocks is automatically and efficiently performed.Seamless integration into an available open-source GIS package.An application to a sample dataset shows method feasibility.