Reservoirs, essential for human water supply, experience thermal stratification affecting water quality. Utilising the CE-QUAL-W2 model, this study simulates thermal stratification and water quality in Shahr Bijar Reservoir, Iran, spanning September 2019 to 2020. Simulations identify the optimal intake gate for selective withdrawal, considering parameters such as dissolved oxygen, phosphate, ammonium, and total dissolved solids. Calibration and validation demonstrate a reasonable correlation between simulated and observed data. Thermal stratification leads to variable water quality at different intake gate levels. Three seasonal management scenarios determine the optimal outlet for selective withdrawal. Results indicate that the third intake gates, with IRWQISC indices of 83.1, 85.5, and 79.8 in fall, spring, and summer, deliver superior-quality water. In winter, all three intake gates, each with an index of 87, exhibit identical quality. This study introduces an innovative approach to reservoir withdrawal optimisation, emphasising seasonal variations and practical implications for water resource management.