Flowpaths are significantly affected by land use change and engineered elements across urban catchments. Conventional GIS-based tools for extracting drainage networks were not developed for urban terrains. This work presents Geo-PUMMA, a GIS toolbox to generate vectorial meshes for terrain representation in distributed hydrological modeling, and to extract drainage patterns in urban and peri-urban catchments. Geo-PUMMA generates well-shaped Hydrological Response Units (HRUs) and Urban Hydrological Elements (UHEs). The toolbox was used in peri-urban catchments of Chile and France to generate three model meshes with different levels of treatment, and extract and compare their corresponding drainage networks. A recommended mesh is identified, which replicates the main morphological and hydrological features of the reference drainage network, and is able to preserve features at small to medium spatial scales (~ 80 - 150 m). Overall Geo-PUMMA can be used to represent the terrain in distributed hydrological modeling applied to urban and peri-urban scales.