Elucidating the origins and transformations of nitrate in groundwater and surface water within agricultural regions is imperative for effectively managing watershed contamination and environmental improvement. This study conducted a comprehensive geochemical investigation using multiple stable isotopes (δD-H2O and δ18O–H2O, δ15N–NO3- and δ18O–NO3-, and δ15N–NH4+) and hydrogeochemical characteristics to explore the potential sources and transformation of nitrate in groundwater and reservoir water within an agricultural riverine reservoir watershed. The results indicated that nitrate pollution in groundwater exhibited a higher severity compared to the reservoir water within this watershed, thereby posing potential risks to the quality of the reservoir water through hydraulic connection. The integration of δ15N–NH4+ and dual-isotopes of nitrate, combined with hydrogeochemical analyses, revealed that the presence of NO3− in groundwater and reservoir water primarily originated from manure/sewage sources. Moreover, intricate biogeochemical processes containing denitrification, nitrification, and DNRA were identified within this watershed. The findings of the Bayesian stable isotope mixing model (SIAR) further corroborated the conclusion that manure/sewage was the primary source of nitrate. It revealed that manure/sewage accounted for an average of 46 % of groundwater NO3− concentration, followed by atmospheric precipitation (25 %), soil nitrogen (18 %), and chemical fertilizer (11 %). There were no distinct differences in nitrate source contributions between groundwater and reservoir water. For reservoir water, manure or sewage (45 % on average) > atmospheric precipitation (28 %) > soil nitrogen (16 %) > chemical fertilizer (11 %). This study demonstrates the effectiveness of incorporating δ15N–NH4+ with dual isotopes of nitrate and hydrogeochemical analyses, serving as a reliable methodology that yields valuable insights into the origins and transformations of NO3− in an agricultural reservoir watershed, with potential applicability to other regions.