In this study, we examined a fish survey method using environmental DNA (eDNA) metabarcoding in a river, and the relationship between the fish survey results and water quality detected in eDNA was analyzed. eDNA surveys and fishing surveys were conducted in summer and winter, targeting three sites on three rivers in Fukuoka prefecture. Our comparison of riffles and pools and our examination of the appropriate places to collect eDNA samples revealed that the detected fish species were not completely consistent between the two kinds of surveys and there was no ecological features common to detected fish species. Therefore, sampling at multiple locations is expected to reduce detectable fish dropouts. More fish species were detected in the eDNA survey than in the collection survey at all times. However, the results also suggested that the DNA of fish species living upstream may remain at sampling site, and benthic fish species tend to be difficult to detect by eDNA surveys. In addition, the influence of water quality on the characteristics of the survey site were analyzed, since marine species were detected in some river eDNA surveys. The results suggested that domestic drainage is likely to affect the characteristics in winter, when the amount of water is small, and the change in concentration of linear alkylbenzene sulfonic acid and its salts and the change of the ratio of chloride ions may be used as an index of domestic drainage.
