Alga as Achnanthes minutissima among diatoms is a widely adaptable taxon on the state of an aquatic environment. In this study, it was found that diatom had a specific tolerance to heavy metals (Cu, Zn, Pb, and Cd etc.) in river water samples, because the diatom assemblage consisted of almost only Achnanthes minutissima in Kakehashi river and Godani river, which were polluted with waste water from Ogoya copper mine. The relationship between the concentrations of heavy metals (Cu, Zn, Pb and Cd) in river water and the attached substances (algae and silt etc.) and the relative abundances of diatom taxa were investigated in detail. The results indicated that the higher is the concentration of heavy metals in the river environment, the higher is only the relative abundances of Achnanthes minutissima. Thus, the taxon can be used as a bioindicator of heavy metal pollution. The relative rates of toxic chemical forms of copper in algae were 61 - 92% in the attached substances and 49 - 70% in the sediment on the river bed, respectively. Therefore, it was found that diatom as Achnanthes minutissima had a tolerance to heavy metals in river water, being able to live in such an environment. Since the water treated with calcium hydroxide from the deposition reservoir of Ogoya mine enters in Godani river, the river is polluted by heavy metals (Cu, Zn, Pb and Cd etc.). From the viewpoint of both biological and chemical analyses, Godani river is still polluted with heavy metals, because their concentrations in the river samples were very high. On the other hand, in Kakehashi river, the concentrations of heavy metals were very low and the distributions of some diatoms appeared in an unpolluted Nishimata river were observed. Therefore, Kakehashi river seems to be considerably recovered from heavy-metal pollution after closing the Ogoya mine.