Intensive lignite and glass sand mining and industrial processing release waste which may contain elements hazardous to the aquatic ecosystem and constitute a potential risk to human health. Therefore, their levels must be carefully controlled. As a result, we examined the effects of sewage on the aquatic Fontinalis antipyretica moss in the Nysa Łużycka (lignite industry) and the Kwisa Rivers (glass sand industry). The Nysa Łużycka and the Kwisa Rivers appeared to be heavily polluted with As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, V and Zn, which were reflected in the extremely high concentration of these elements in F. antipyretica along the studied watercourses. In the Nysa Łużycka, trace element composition in the moss species is affected by lignite industry with accumulation in its tissues of the highest concentrations of Cd, Co, Cr, Cu, Mn, Ni, Pb and Zn, while samples from the Kwisa sites influenced by glass sand industry revealed the highest concentrations of As, V and Fe. The principal component and classification analysis classifies the concentration of elements in the aquatic F. antipyretica moss, thus enabling the differentiation of sources of water pollution in areas affected by mining industry.