The aim of this research was to assess the impact caused by a long-term pollution by fluoride and heavy metals in two soils (PS1 and PS2) near an aluminium smelter in Slovakia, on soil microbial biomass C (MBC), basal respiration, metabolic quotient (qCO2) water-soluble organic C (WSOC) and enzymes activities involved in the C, N and P biogeochemical cycles. An unpolluted soil was used as control (C0). Results obtained for soil fluoride content reflected a gradient of fluoride exposure in topsoils of contaminated sites. Decreases in microbial and enzymatic activities and in MBC to organic C ratio were found in PS2 site, which is closer to the smelter and exhibited the highest fluoride content. PS1-soil showed an extreme alkaline pH caused by leaching of waste effluents from the smelter dumping site, higher contents of Zn, Cu, Pb and Cd, significantly larger MBC, qCO2 and catalase and urease activities, and much larger basal respiration and dehydrogenase activity than PS2 and C0-soil. Phosphatase, β-glucosidase and BAA-protease were negatively correlated with WSOC, basal respiration and dehydrogenase activity, and showed some degree of inhibition in polluted sites. These results may indicate different responses of microbial communities to ecosystem disturbances, caused by the drastic changes in soil's physicochemical properties as result of the long-term emissions of fly ash with high levels of contaminants that are still affecting soil microbial and enzymatic activities.