This study evaluated the seasonal performance of the Koka water treatment plant in removing natural organic matter (NOM) and the implications for disinfection by-product (DBP) formation potential. Raw and treated water samples were collected during the dry and wet seasons and analyzed using physicochemical parameters and fluorescence spectroscopy. The results revealed significant seasonal variations in raw water (RW) quality, with higher turbidity, pH, temperature, conductivity, total organic carbon (TOC), dissolved organic carbon (DOC), and UV254 absorbance during both seasons and across treatment processes. The overall NOM removal efficiency of the treatment plant was poor, with mean TOC removal of 46 and 43% and DOC removal of 15.8 and 15.2% during dry and wet seasons, respectively. The sedimentation unit demonstrated negative TOC removal, indicating NOM accumulation likely due to biochemical reactions in the unit. Fluorescence analysis and the correlation between specific ultraviolet absorbance (SUVA) and DBP formation potential suggest a higher risk of DBP formation in chlorinated drinking water. These findings highlight the influence of seasonal variations, RW quality, and the treatment process dynamics on the plant's performance in removing NOM. There is a need to implement adaptable strategies to enhance NOM removal, accounting for seasonal fluctuations in RW quality.