Although 3-D geological modeling has been mostly employed in the prospection and exploitation of ores, oil and gas, its importance in the field of groundwater resources management is considerably increasing. Traditional 3-D geological modeling schemes are based on explicit digitization of geological units and structures. Progresses in 3-D interpolation techniques have favored the emergence of implicit modeling, in which geological surfaces are automatically created from hard data and interpretation. The major benefit of implicit modeling relies on its speed. In this work the implicit modeling approach was applied to conceptualize and model a karst aquifer in southwest Germany, using digital elevation data, geological maps, borehole logs, and geological interpretation. Dip and strike measurements as well as soil-gas surveys of mantel-borne CO2 were conducted to verify the existence of a postulated fault. The geological model was automatically translated into a numerical groundwater flow model that was calibrated to match measured hydraulic heads, spring discharge rates, and flow directions observed in tracer tests. Refinements of the numerical model’s spatial parametrization was iteratively conducted, using the geological model for visualization of interim simulations. As the results of numerical modeling may support or contradict the 3-D geological model, additional geological insights can be eventually gained in this way. The geological model allowed the proper assessment of the system geometry and the definition of boundary conditions. The numerical groundwater flow model was applied to evaluate the potential risks from limestone quarries to local water supply wells.