The feasibility of using a Ground-Penetrating Radar (GPR) to obtain river cross-sections was verified by many researches. In Taiwan, the Sediment Concentration (SC) in rivers is always in the order of several hundred parts per million, which increases to more than 30,000 ppm during rainfall. The water depth calculated using GPR may be influenced by the SC as the radio waves pass through the water volume. In this study, we investigated the effects of SC on the transmittance ability of GPR signals. The clay in the Shihmen reservoir was preliminarily used as the sediment material. The SC ranged from freshwater to 35,759 ppm, and the experiments were conducted at two temperature ranges. The results indicated that the water depth measured using GPR was strongly affected by the SC and the water temperature. We recommend that such data as the chemical properties of the sediment, SC, and water temperature in the field be recorded when measuring the cross-section by using GPR.