A methodology for groundwater evaluation has been developed by the combined use of numerical model and spatial modeling using GIS. The developed methodology has been applied on the sub-basin of the Banganga River, India. Initially, the groundwater potential zones have been delineated by spatial modeling. Different thematic maps of the basin like geology, geomorphology, soil, drainage, slope factor and landuse/landcover have been used to identify the groundwater potential zones. Further, the groundwater flow model for the study area has been developed in the MODFLOW. The groundwater flow vector map has been developed and superimposed on the potential zone map to validate the results of spatial modeling. Finally, the different scenarios have been conceptualized by varying the discharge of the wells and purposing the location for new rainwater harvesting structures. Results reveal that increasing the discharge of the wells in the potential zones put less stress on the aquifer. The suggested locations of rainwater harvesting structures also help to reduce the overall decline of groundwater in the area. The hydrological and spatial modeling presented in this study is highly useful for the evaluation of groundwater resources and for deciding the location of rainwater harvesting structures in semi-arid regions.