Surplus nutrient load and complex migration and transformation processes are the challenges for water quality management in the peri-urban coastal watershed, leading to increasing concerns worldwide. We investigated the spatio-temporal variation of hydrogeochemical parameters in surface water of Jimei Lake watershed, and distinguished the sources and transformation of nitrate-N (NO3−-N) using dual isotopes of nitrate (δ15N and δ18O in NO3−) with hydrogeochemical indicators. Principal component analysis (PCA) on hydrogeochemical parameters demonstrated that surface water was seriously polluted by nutrients, especially in the southeast of the downstream. There were signs of seawater intrusion and increased wastewater discharge in the mid-lower reaches with high ammonium concentrations. Nitrification occurred throughout the monitoring period with lower δ15N and δ18O values and NO3− derived from mixed pollution sources. Results of Bayesian model showed that dominant NO3− input originated from manure and sewage (M&S, 71% and 76% in the wet and dry season, respectively) and atmospheric deposition (22% and 16%, respectively). This result implied that the controls and treatment of M&S discharges are essential to alleviate of NO3− pollution. The proposed method is helpful to understand the origins of NO3− and may be suitable to develop measures for the reducing of nitrogen loadings in the peri-urban watershed. Display omitted •MixSIAR model revealed no significant seasonal difference in NO3− pollution.•Reveal the degree and difference of water pollution by using PCA in peri-urban area.•Relationships between lower δ15N values and nutrients implied nitrification occurred.•Manure and sewage were the main NO3− sources of Jimei Lake.