This study evaluates the impacts of construction activities from the Ulu Jelai Hydroelectric Project on the water quality of the Susu Reservoir, a critical freshwater system in Malaysia fed by the Telom, Mensun, Bertam, Menlock, Lemoi, and Tekai rivers. A systematic spatial–temporal analysis was conducted using 15 water quality monitoring stations (WQ1–WQ18), strategically distributed across tributaries, inflow points, and the Susu Dam. Key physicochemical, biological, and hydrological parameters, including turbidity, total suspended solids (TSS), pH, dissolved oxygen (DO), ammonia (NH₃-N), E. coli, and oil and grease (O&G), and flow rate, were analyzed across wet and dry seasons. The results revealed significant seasonal variability in water quality parameters. Dry periods were characterized by elevated DO, O&G, and flow rate levels with an average of 8.98 mg/L, 1932.98 mg/L, and 7.48 m³/s, respectively, alongside reduced TSS and E. coli with an average of 300.23 mg/L and 656.47 CFU/100mL, respectively. In contrast, wet seasons exhibited heightened turbidity, BOD, and nutrient influx, with an average of 201.73 NTU, 1.84mg/L, and 0.16 mg/L, due to runoff within the Upper Susu Watershed. Principal component analysis (PCA) attributed dry-season conditions to climatic and physicochemical drivers, whereas wet-season water quality degradation correlated with anthropogenic activities, such as agricultural runoff, livestock operations, and rainfall conditions. Turbidity levels exceeded regulatory thresholds at multiple monitoring stations, underscoring localized sediment mobilization near construction zones. The findings underscore the cumulative impacts of land-use practices and hydroelectric infrastructure on reservoir integrity. Elevated contaminant levels, driven by seasonal hydrological dynamics and anthropogenic pressures, necessitate adaptive management strategies. This study provides a framework for balancing hydroelectric development with ecological sustainability in tropical montane systems, emphasizing evidence-based practices to minimize anthropogenic degradation in freshwater reservoirs.