Sedimentation limits the benefits of storage reservoirs, especially in areas with higher sediment yields, such as Agongdian Reservoir in southern Taiwan. Although drawdown flushing is a known strategy that releases large amounts of fine sediment into a downstream channel, there is limited information on the long-term monitoring and multiple metrics being used to evaluate flushing efficiency. The objectives of this study were three-fold: (1) to continue collecting valuable long-term observed data, since Agongdian Reservoir is one of the few reservoirs currently conducting sediment flushing operations; (2) to evaluate and identify the hydrological parameters that are highly related to the flushing efficiency; (3) to execute numerical simulations of different reservoir flushing scenarios at multiple water levels to discuss potential strategies to improve the flushing efficiency. The findings of this study revealed that long-term monitoring data was valuable for identifying factors highly related to the flushing efficiency, which included the initial water level; average water level; average velocity. Based on simulations, compartmentalizing the reservoir is a proposed strategy that has demonstrated high levels of improvement in terms of the flushing efficiency, depending on particular scenarios involving partition desilting, empty flushing, or a combination of both. Recommendations to increase the flushing efficiency include lowering the initial water level, creating a narrower gorge-like geometry by partitioning, and further considering to modify the operation rules.