The contribution of selected pesticides to the mutagen formation potential (MFP) of river waters was studied. The concentrations of the pesticides in river water samples were determined by means of a quadrupole GC-MS. Twelve out of 39 pesticides measured were detected in the water samples collected from Kotsuki River. Ames mutagenicity assays (preincubation method) using Salmonella typhimurium TA100 without metabolic activation by S9 mix (TA100-S9) were performed to measure the MFP. From all the samples collected, significant MFPs were detected. The maximum contribution of the pesticides to the MFP of the river water samples was 0.11%, indicating that the effect of the pesticides found in this study on the MFP of the river water samples is insignificant. The contribution of pesticide degradation products to the MFP of river waters should be investigated in order to see whether pesticide degradation products affect the MFP of river waters.