Groundwater is a dynamic and replenishable natural resource. The numerical modeling techniques serve as a tool to assess the effect of artificial recharge from the water conservation structures and its response with the aquifers under different recharge conditions. The objective of the present study is to identify the suitable sites for artificial recharge structures to augment groundwater resources and assess its performance through the integrated approach of Geographic Information System (GIS) and numerical groundwater modeling techniques using MODFLOW software for the watershed located in the Kodaganar river basin, Dindigul district, Tamil Nadu. Thematic layers such as geology, geomorphology, soil, runoff, land use and slope were integrated to prepare the groundwater prospect and recharge site map. These potential zones were categorized as good (23%), moderate (54%), and poor (23%) zones with respect to the assigned weightage of different thematic layers. The major artificial recharge structures like percolation ponds and check dams were recommended based on the drainage morphology in the watershed. Finally, a three-layer groundwater flow model was developed. The model was calibrated in two stages, which involved steady and transient state condition. The transient calibration was carried out for the time period from January 1989 to December 2008. The groundwater model was validated after model calibration. The prediction scenario was carried out after the transient calibration for the time period of year up to 2013. The results show that there is 15 to 38% increase in groundwater quantity due to artificial recharge. The present study is useful to assess the effect of artificial recharge from the proposed artificial structures by integrating GIS and groundwater model together to arrive at reasonable results.