The unsteady flow in the Middle Route South-to-North Water Transfer Channel was simulated numerically using an implicit solution procedure for the Saint Venant equations. An equivalent roughness was used to simulate the effect of many transfer structures on the water levels in the main channel. Various gate operating and control methods were analyzed to study the response to disturbances produced by varying the flow rates through the Tianjin outlet. The results show that when the inflow at the head changes in the same way as the sum of the flow rates through all the outlets, the transition time and the fluctuation of the water levels using the timed gate operation method are less than when using the simultaneous gate operation method, but the variations of the gate openings and flow rates through each control gate are much larger. The flow disturbances produced by the Tianjin outlet can be rectified within several channel sections and the transition time can be greatly shortened by allowing the water levels immediately upstream of the control gates to vary within proscribed ranges, rather than being held constant. The unsteady flow in the Middle Route South-to-North Water Transfer Channel was simulated numerically using an implicit solution procedure for the Saint Venant equations. An equivalent roughness was used to simulate the effect of many transfer structures on the water levels in the main channel Various gate operating and control methods were analyzed to study the response to disturbances produced by varying the flow rates through the Tianjin outlet. The results show that when the inflow at the head changes in the same way as the sum of the flow rates through all the outlets, the transition time and the fluctuation of the water levels using the timed gate operation method are less than when using the simultaneous gate operation method, but the variations of the gate openings and flow rates through each control gate are much larger. The flow disturbances produced by the Tianjin outlet can be rectified within several channel sections and the transition time can be greatly shortened by all owing the water levels immediately upstream of the control gates to vary within proscribed ranges, rather than being held constant.