The transport timescales were investigated in response to water level variation under different constant flow rates in Dahuofang Reservoir. The concept of water age was applied to quantify the transport timescales. A three-dimensional hydrodynamic model was developed based on the Environmental Fluid Dynamics Code (EFDC). The model was calibrated for water surface elevation and temperature profiles from April 1, 2008 to October 31, 2008. Comparisons of observed and modeled data showed that the model reproduced the water level fluctuation and thermal stratification during warm season and vertical mixing during cold season fairly well. The calibrated model was then applied to investigate the response of water age to water level changes in Dahuofang Reservoir. Model results showed that water age increases from confluence toward dam zone. In the vertical direction, the water age is relatively uniform at upstream and stratifies further downstream, with a larger value at bottom layer than at surface layer. Comparisons demonstrated that water level variation has a significant impact on transport timescales in the reservoir. The impact of water level drawdown on water age is stronger at bottom layer than at surface layer. Under high flow conditions, the water age decreases 0–20 days at surface layer and 15–25 days at bottom layer. Under mean flow conditions, the water age decreases 20–30 days at surface layer and 30–50 days at bottom layer. Furthermore, the impact is minor in the upstream and increases further downstream. The vertical stratification of water age weakens as the water level decreases. This study provides a numerical tool to quantify the transport timescale in Dahuofang Reservoir and supports adaptive management of regional water resources by local authorities.