Nitrate is one of the primary nutrients associated with sedimentation and fuels eutrophication in reservoir systems. In this study, water samples from Bukit Merah Reservoir (BMR) were analysed using a combination of water chemistry, water stable isotopes (δ2H-H2O and δ18O-H2O) and nitrate stable isotopes (δ15N-NO3- and δ18O-NO3-). The objective was to evaluate nitrate sources and processes in BMR, the oldest man-made reservoir in Malaysia. The δ15N-NO3- values in the river and reservoir water samples were in the range +0.4 to +14.9‰ while the values of δ18O-NO3- were between -0.01 and +39.4‰, respectively. The dual plots of δ15N-NO3- and δ18O-NO3- reflected mixing sources from atmospheric deposition (AD) input, ammonium in fertilizer/rain, soil nitrogen, and manure and sewage (MS) as the sources of nitrate in the surface water of BMR. Nitrate stable isotopes suggested that BMR undergoes processes such as nitrification and mixing. Denitrification and assimilation were not prevalent in the system. The Bayesian mixing model highlighted the dominance of MS sources in the system while AD contributed more proportion in the reservoir during both seasons than in the river. The use of δ13C, δ15N, and C:N ratios enabled the identification of terrestrial sources of the organic matter in the sediment, enhancing the understanding of sedimentation associated with nutrients previously reported in BMR. Overall, the nitrate sources and processes should be considered in decision-making in the management of the reservoir for irrigation, Arowana fish culture and domestic water supply.