Several small reservoirs and a large number of check dams had been constructed in theWangkuai reservoirwatershed after 1970s, and flood time series lacked stationarity, which affected the original design floodhydrographs for the Wangkuai reservoir. Since the location, storage capacity and drainage area of thelarge number of check dams were unknown, we present a method to estimate their total storage capacities(TSC) and total drainage areas (TDA) by using the recorded rainstorm and flood data. On the basisof TSC and TDA, the flood events which occurred in an undisturbed period were reconstructed undercurrent conditions to obtain a stationary flood series. A frequency analysis was subsequently performedto assess the design flood peak and volume for both small and medium design floods with a 10–200year return period. For large and catastrophic floods, it was assumed that the upstream check dams andsmall reservoirs would be destroyed, and water stored in these hydraulic structures were re-routed to theWangkuai reservoir by unit hydrograph. The modified flood peak and volume decreased for floods witha 10–200 year return period when compared to the current design flood. But for large design floods witha return period exceeding 500 years, peak discharge increased. This study provides a new method fordesign flood calculation or modification of the original design flood in watersheds with a large numberof check dams.