The existence of pharmaceuticals in the water environment is thought to be a potential problem for aquatic organisms. In this study, we conducted a nationwide survey to clarify the occurrence of 24 selected pharmaceuticals in major Japanese rivers and evaluated their environmental risk to aquatic organisms. We found a total of 22 substances in river waters at concentrations from several nanograms per liter to several micrograms per liter. We found the highest, which was 2.4 μg/L of caffeine, followed by 1.5 μg/L of crotamiton and 1.4 μg/L of sulpiride. We conducted an environmental risk assessment of the 22 pharmaceuticals detected in river water, for which predicted no-effect concentration (PNEC) values for crustacea and algae had been obtained. The measured environmental concentration/PNEC values of four substances, caffeine, carbamazepine, clarithromycin, and ketoprofen, exceeded 0.1 with the maximum value of 9.0 for clarithromycin. As clarithromycin exhibits a high environmental risk to aquatic organisms, particular attention is required.