An investigation to high temperature geothermal water in Kawu Village of Sakya County, Tibet was made. We found that harmful elements in geothermal water whose concentrations were far higher than the limits of class Ⅱof “environmental quality standard of surface”(GB3838—2002) and the safety limits of “Drinking Water Quality Standards”(the second edition) were F、B、As、Sb、Tl、Be, while radioactive toxic elements are mainly Th, U. We analyzed the concentration variation of harmful elements before and after Chongqu River flows through the geothermal area with line charts and the Nemerow index method. The results show that geothermal water seriously affects the water quality of Chongqu River. In the end, some useful suggestions about the utilization of geothermal water were put forward.