Groundwater degradation through abstraction, contamination, etc., shows a world-wide increase and has been of growing concern for the past decades. In this light, the stable isotopes of the water molecule (d18O and d2H) from a hard-rock aquifer in the Maheshwaram watershed (Andhra Pradesh, India) were studied. This small watershed (53 km2) underlain by granite, is endorheic and representative of agricultural landuse in India, with more than 700 bore wells in use. In such a watershed, the effect of overpumping can be severe and the environmental effects of water abstraction and contamination are of vital importance. A detailed and dynamic understanding of groundwater sources and flow paths in this watershed thus is a major issue for both researchers and water managers, especially with regards to water quality as well as the delimitation of resources and long-term sustainability. To this end, the input from monsoon-precipitation was monitored over two cycles, as well as measuring spatial and temporal variations in d18O and d2H in the groundwater and in precipitation. Individual recharge from the two monsoon periods was identified, leading to identification of periods during which evaporation affects groundwater quality through a higher concentration of salts and stable isotopes in the return flow. Such evaporation is further affected by land-use, rice paddies having the strongest evapotranspiration.