We quantified nitrate (NO3−), chloride (Cl−) and water hardness concentrations in stream water catchments in the Koza River within the Shimanto Belt, where low nitrate concentrations in precipitation are reported. We conducted water sampling at nine sites in the Koza River’s stream waters in southern Wakayama at ordinary water levels, and the elevations range from 35 to 410 m. The mean concentrations of nitrate and chloride of the samples were 90.7 μM and 4.27 μM, respectively. The mean water hardness concentration was 9.12 mg L−1, which is significantly low values. These results show that the chloride concentrations in stream water catchments had the elevation dependency. The nitrate concentrations in stream waters of the Koza River were substantially low, and the samples fell below the detectable limits in the upper reaches of the Shichikawa Dam in summer. Thus, sampling of stream water catchments in the Koza River can be used as control to monitor cross-border pollution in Japan.