The importance of groundwater in preserving the health of water resources such as rivers, lakes, streams, and associated vegetation is often ignored or underestimated, which shows a lack of groundwater management policies. Therefore, in order to manage and protect groundwater and groundwater-dependent ecosystems (GDEs), a complete framework is needed, which is necessary for accomplishing the sustainability aim. The present study utilized remote sensing-based input, in-situ data, and a GIS framework for mapping and validation of GDEs. The weights of the input layers were assigned using experts’ opinions. In the study area, GDEs are heterogeneous, and the impact of groundwater overdraft on its dependent ecosystems was also assessed using long-term in–situ groundwater level data. The results show a decreasing trend in groundwater storage; many wells have dried in recent years, whereas surface runoff through the natural streams is also reduced, which reduces the supply of water and the need to identify new well locations. The validation of GDEs shows an accuracy of 73.40% through the area under the curve method. Further, the GDEs map was categorized into five classes, and the moderate GDEs are the dominant in the area. The study shows an overall decrease in vegetation over the past two decades. Considering the risks of groundwater overdraft, the policy implications to support the conservation of GDEs within a sustainable withdrawal context have also been discussed in this work.