Deposits of coal combustion wastes, especially fly ash, are sources of environmental and health risks in industrial regions. Recently, fly ash deposits have been reported as habitat surrogates for some threatened arthropods in Central Europe. However, the potential environmental risks of fly ash have not yet been assessed in the region. We analysed concentrations of 19 minor and trace elements in 19 lignite combustion waste deposits in the Czech Republic. We assessed their environmental risks by comparison with the national and EU legislation limits, and with several commonly used indices. Over 50% of the samples exceeded the Czech national limits for As, Cu, V, or Zn, whilst only V exceeded the EU limits. For some studied elements, the high-risk indices were detected in several localities. Nevertheless, the measured water characteristics, the long-term presence of fly ash, previous leaching by acid rains, and the low amount of organic matter altogether can infer low biological availability of these elements. We presume the revealed high concentrations of some heavy metals at some studied sites can be harmful for some colonising species. Nevertheless, more ecotoxicological research on particular species is needed for final decision on their conservation potential for terrestrial and freshwater biota.