The Chakari alluvial aquifer is the primary source of water for human, animal, and irrigation application. In this study, the geochemistry of major ions and stable isotope ratios (δ2H-H2O, δ18O-H2O, δ15N-NO3̄, and δ18O-NO3̄) of groundwater and river water samples from the Chakari Plain were analyzed to better understand characteristics of nitrate. Herein, we employed nitrate isotopic ratios and BSIMM modeling to quantify the proportional contributions of major sources of nitrate pollution in the Chakari Plain. The cross-plot diagram of δ15N-NO3̄ against δ18O-NO3̄ suggests that manure and sewage are the main source of nitrate in the plain. Nitrification is the primary biogeochemical process, whereas denitrification did not have a significant influence on biogeochemical nitrogen dynamics in the plain. The results of this study revealed that the natural attenuation of nitrate in groundwater of Chakari aquifer is negligible. The BSIMM results indicate that nitrate originated mainly from sewage and manure (S&M, 75‰), followed by soil nitrogen (SN, 13‰), and chemical fertilizers (CF, 9.5‰). Large uncertainties were shown in the UI90 values for S&M (0.6) and SN (0.47), whereas moderate uncertainty was exhibited in the UI90 value for CF (0.29). The findings provide useful insights for decision makers to verify groundwater pollution and develop a sustainable groundwater management strategy.