Agricultural activity in the Pushkar Valley, Rajasthan is constrained due to limited availability of good quality water. In this context, occurrence of nitrate and fluoride in the groundwater was investigated and reported. Integration of stable isotope (δ18O) data with recharge characteristics (based on 3H-tracer studies) helps in clearly characterizing the processes controlling contamination by point and non-point sources. High nitrate and fluoride groundwaters are associated with high δ18O waters. This indicates that significant quantities of evaporated (isotopically enriched) surface run-off water and rain water infiltrate along with nitrate and fluoride salts in the soil. The applicability of this approach under different hydrometeorological conditions is also confirmed.