Geomodelr is an online platform for geological modeling that allows visualizing the disposition of different geological, hydrogeological, lithostratigraphic and/or structural units in an interactive and three-dimensional way. Its flexibility allows the generation of 3D hydrogeological conceptual models that can be exported to FEFLOW and MODFLOW regardless the complexity of the project using an adaptive approach or "Smart-layering" or full “Unstructured” conditions to build the geometry. Besides, during geological model construction, the user can include rivers or wells and create meshes with automatic assignment of hydraulic properties (i.e., K, Ss) with element and node selections and local refinements generated in the domain. To achieve such objective, we will implement a model applied to a real case in Úmbita, Boyacá, Colombia, where the geology is complex due to the structural system and lithologies in the zone. Our results show that the geometry built in Geomodelr satisfies the interpretation of the geologists, and the mesh exported keeps with great precision the geometrical forms facilitating the job of the hydrogeologist when generating groundwater numerical models with high-quality.