The study aims to characterise the changes in elemental composition in the river sediments of streams influenced by mine waters enriched with radionuclides. The study took place in the vicinity of Ostrava, a city located in a coal mining region in the Czech Republic, namely the Upper Silesian Coal Basin. River sediments and waters of the Karvinský potok and Stružka streams were investigated. Field measurements were made for ambient dose equivalent rate (ADER). Laboratory gamma spectrometry and X-ray fluorescence were used to determine the content of radionuclides and elemental composition in river sediments. Water samples were analysed for the content of major ions and radionuclides. The field ADER measurement proved elevated content of radionuclides with values exceeding 1,000 nSv/h in both streams. The discharged mine waters were Na–Cl type, containing an 226Ra (0.68–0.70 Bq/l) as a dominant radionuclide. Laboratory measurements of radionuclides in bottom sediments proved that the prevailing source of radiation are 226Ra and 232Th in both streams. The calculated enrichment factors showed extreme values for Sr, Cr, Pb, Zn, Cu, and Mo. The precipitation reactions forming Ca-minerals (calcite and aragonite), Fe-bearing minerals (hematite, goethite and amorphous Fe(OH)3) and hausmannite were found to be the primary geochemical process underway in the studied riverine systems. The correlation between elements and radionuclides demonstrated the significant role of geochemical barriers that lead to the precipitation of radionuclides from solution. The results show that the precipitation takes place preferentially in places where other waters enter the stream, or where recent organic matter is present.