Organic matter in lakes is categorized into allochthonous organic matter, such as leaves and sewage effluent, and autochthonous organic matter, generated by microorganisms within the water system. In this study, organic matter composition was analyzed using UV-vis spectroscopy and liquid chromatography-organic carbon detection (LC-OCD). Several allochthonous natural organic matter substances were collected including leaves, green leaves, forest soils, and paddy soils. The organic matter composition analysis in our study sites revealed that humic substances comprised the highest proportion (36.5–42.3%). Also, individual samples at each site exhibited distinct characteristics. This study used a humic substance-diagram (HS-diagram) and principal component analysis (PCA) to trace the sources affecting the river water quality and identify their origins. The humic substances of soil origin predominantly influenced the water quality, with the impact of organic matter significantly pronounced during the July rainfall period. Compared with the PCA results, the contribution of the humic substance (HS, 48.9%) and building block (BB, 42.0%) indices appeared higher between June and July in summer, likely due to non-degradable substances released by heavy rain. In fall, the contribution of low molecular weight neutrals increased from 71.2% to 85.2%, owing to a humic substance influx and decomposition. This study demonstrated the application of estimating the relative contributions of source materials in lakes utilized for drinking and agricultural water to identify sources, aiding in the development of efficient watershed management plans.