This study investigates the spatiotemporal patterns and driving factors of surface water chemistry in the Mudong River Basin, Guilin, combining hydrological monitoring, principal component analysis (PCA), and nitrate dual-isotope tracing. Results indicate that: (1) Total nitrogen (TN) is the primary pollutant, with a 70.6% exceedance rate, showing significantly higher concentrations in the dry season. Spatially, the northern recharge area exhibited the highest NO₃⁻-N/TN ratio, while total phosphorus (TP) accumulated along the flow path in the western discharge area. (2) PCA identified three key dimensions governing water quality: hydro-physical status (water temperature vs. dissolved oxygen), nutrient load (TN/TP), and hydrodynamic conditions. (3) Crucially, a fundamental seasonal shift in nitrate sources was revealed Bayesian source apportionment: sewage manure dominated in the dry season (37.9%), while soil organic-N (became the primary source in the rainy season (63.1%). These findings highlight the seasonal dynamics of pollution sources and are vital for formulating targeted water management strategies.