Increasing manganese (Mn) concentrations in source water contribute to aesthetic and health-related concerns in drinking water. The challenges with Mn in drinking water primarily arise from elevated Mn concentrations in the water supply reservoir, with the inefficacy of Mn treatment largely attributed to fluctuating Mn levels in the water source. A three-dimensional Mn cycle model in a temperate monomictic reservoir, Tarago Reservoir, and a decision support system reflecting Mn variations in the local water treatment plant have been established in previous research. This study aimed to examine Mn variations from the reservoir to raw water and treated water under the influence of wind conditions during different stages of thermal structure, and discover valuable recommendations for Mn treatment in the local water supply system. We crafted 12 scenarios to scrutinize the impact of varying intensities of offshore and onshore winds on hydrodynamic processes and Mn transport during strong thermal stratification, weak thermal stratification, and turnover. The scenario analysis revealed that, during the gradual weakening of thermal stratification, offshore wind induced a substantial amount of Mn to the upper layers near the water intake point. Conversely, onshore wind hindered the upward transport of Mn. The simulated Mn in the raw water under the 12 scenarios indicated that the timing of turnover in the Tarago Reservoir is the primary concern for Mn treatment in the water treatment plant. Additionally, close attention should be given to the frequency and intensity of offshore winds during the weakening of thermal stratification.