The hydrochemical characteristics and nitrate nitrogen–oxygen isotopes of lake water systems provide critical insights for identifying nitrate pollution sources and elucidating their formation mechanisms. This study investigated the Poyang Lake Basin using an integrated approach combining graphical analysis, statistical modeling, and Bayesian inference, based on 26 surface water and 31 groundwater samples collected in November 2019. The results revealed complex hydrochemical diversity in the study area, with HCO3-Ca type water dominating both surface water (92.3%) and shallow groundwater (83.9%). While surface water originated primarily from atmospheric precipitation, shallow groundwater showed additional influences from water–rock interactions and cation exchange. Carbonate rocks, evaporites, and silicates constituted the primary anion sources for groundwater. Surface water nitrate exhibited strong positive correlations (r = 0.54–0.93) with TDS, HCO3−, Cl−, SO42−, and major cations (K+, Ca2+, Na+, Mg2+). In contrast, groundwater nitrate demonstrated weaker correlations (r = 0.31–0.63) with these parameters, suggesting more intricate formation processes. Neither nitrification nor denitrification significantly influenced basin water chemistry. Source apportionment analysis identified soil nitrogen (45.2%) as the dominant nitrate contributor in surface water, followed by atmospheric deposition (28.1%), agricultural fertilizers (19.7%), and domestic waste (7.0%). These findings establish a theoretical foundation for ecological management and nitrate pollution control through comprehensive hydrochemical characterization and pollution source identification.