Aquifer based hydro geological investigation is most important part in watershed development program. This is the scientific and more effective method for implementation of watershed programs. In many parts of India, aquifers hold limited storage capacities therefore we cannot use same treatment for all watershed programs. Aquifers in different hydrogeological settings relate differently to watersheds. Using Aquifer based investigation we can find out the recharge and discharge zones and it helps to construct harvesting structures on perfect locations as a result the chances of rainwater recharge is more effective and fruitful.