The regulation of the tail water level of Shuikou hydroelectric station will need at least 3.5 years. Based on the arrangement conditions of water level treatment hinge and navigation conditions of the construction reach, through theoretical analysis and model experiment, we propose the navigation guaranteeing measures which combine waterway dredging, reef explosion for barrier clearance with scientific station dispatch. The results indicate that the navigation reliability is lower in the partly time intervals of the two dry seasons, during the construction time of second and fourth stage cofferdam. However, during other construction periods, the navigation reliability is more than 85%. The navigation measures are proposed to ensure the shipping in Minjiang river is unimpeded during construction.