Abstract: As one of the eight major outlets of the Pearl River, Jitimen serves as a crucial conduit for the transport of land-based pollutants from the Pearl River Delta urban agglomeration to the ocean, significantly impacting the ecological and environmental quality of the river basin and adjacent marineareas. The Jitimen waterway is characterized by large runoff during flood seasons and strong tidal currents during dry seasons. Conducting pollution source tracing during the flood seasons is essential for accurately identifying land-based pollution sources. This study focused on the Jitimen waterway, where samples were collected from the main stem and tributaries during the 2022 flood season. By integrating routine water quality parameter analysis, 3-dimensional excitation-emission matrix fluorescence (3D-EEMs) characteristic analysis of dissolved organic matter (DOM), and multi-parameter correlation analysis, we investigated and analyzed the sources and processes of water pollution and identified key pollution areas. The results show that the mainstream water quality generally meets Class Ⅱ of the Environment Quality Standards for Surface Water (GB 3838-2002), but various parameters fluctuate along the flow direction. The upstream segment exhibits strong self-purification capacity, while the downstream segment, influenced by tributaries inflows, shows an initial decline followed by an increase in total nitrogen (TN), ammonia nitrogen (NH₃-N), and chemical oxygen demand (COD). The overall water quality of tributaries is relatively poor, with higher concentrations of TN, NH₃-N, and total phosphorus (TP) in circular tributaries flowing through residential and aquaculture zones. 3D-EEMs reveal that organic pollutants in the mainstream are primarily composed of tyrosine-like, fulvic acid-like, and degradation intermediates, and notable increase in fluorescence abundance was observed in the M1-M3 and M4-M6 segments. M2, M5 and M6 were marked as hotspots for pollutant discharge. The fluorescence abundance of DOM in tributaries is 9.5 times that of the mainstream, with protein-like substances and terrestrial humus as the main contributors. Fluorescence index analysis shows that mainstream pollutants originate primarily from terrestrial inputs, while tributaries exhibit a combination of terrestrial and autochthonous inputs. By integrating routine water quality parameter analysis, we identified that tributary points T5 and T7 exhibit characteristics of domestic sewage, and T14 and T16 exhibit characteristics of aquaculture wastewater. Multiple points on the circular tributaries T2, T4 and T10 display autochthonous characteristics due to gate control influence. Multi-parameter correlation analysis further supports these results, and targeted control measures are recommended for management.