While normally monitoring the Shinano River water quality, including examinations for mutagenicity, the Niigata Chuetsu Earthquake suddenly occurred on October 23, 2004. However, the influence of this earthquake on the mutagenicity of river water has not yet been well studied. To clarify the regional and seasonal changes in mutagenicity of the Shinano River water, blue rayon was suspended for 24 hrs at 4 sampling sites, once a month from September 2004 through August 2005. Mutagenicity was evaluated by the Ames test using Salmonella typhimurium TA98 (TA98) and TA100 with or without metabolic activation by S9 mixture. To detect and identify poly-aromatic hydrocarbons that may be responsible for the mutagenicity of the river water, we analyzed benzo[a]pyrene, benzophenone, 4-nitrotoluene, or other compounds using gas chromatography-mass spectrometry and total ion chromatogram spectra. Positive manifestations of TA98 with S9 mixture were observed at the 4 sampling sites throughout the 12-month test, showing a tendency to be higher at the downstream site and in winter. However, the highest mutagenicity was observed in the sample collected at the most upstream sampling site in December 2004, and fluoranthene or pyrene consisting mainly in coal tar was detected only in the samples collected in December 2004. Although benzo[a]pyrene, benzophenone, and 4-nitrotoluene were below the detection limits, non-mutagens such as aliphatic hydrocarbons or esters were frequently detected. Our findings indicate that either fluoranthene or pyrene was mainly responsible for the mutagenicity of the river water in December 2004, suggesting the possibility of oil contamination caused by the Niigata Chuetsu Earthquake.