This paper presents a hydraulic performance graph model in which the flow carrying capacity of a channel system was determined by accounting the interacting backwater effect among channel reaches and incoming lateral flow. The method utilizes hydraulic performance graphs (HPGs), and the method is applied to a natural channel Nakdong River to examine its applicability. This research shows that estimation results using HPG are close to records from the stage station and the results from a widely-accepted model, HEC-RAS. Assuming that a water level gage site is ungaged, water level estimations by HPGs compared with observation show that with a flood event, the HPGs underestimate in the water level ascension phase, but in the recession phase they overestimate results. The accuracy of estimation with HPGs was greatly improved by considering the time difference of flooding between the observation and estimation locations.