The Stráž pod Ralskem region is a part of the Bohemian Cretaceous Basin. The geological profile of the site consists of Quaternary river sediments, Middle Turonian sandstone, Lower Turonian siltstone and Cenomanian collector formed by friable sandstone containing uranium bearing minerals and upper fucoid sandstone forming an overlying back of the ore. The uranium deposit Stráž was exploited by underground acidic leaching between 1968 and 1996. More than 14 000 tons of uranium were produced during this period. Minimum 4 million tons of H2SO4, 300 thousand tons of HNO3, 120 thousand tons of NH3 and other chemicals were injected into the Cenomanian sandstones. The chemical mining of uranium resulted in a large contamination of the groundwater collectors in Stráž block of North Bohemian cretaceous table and caused serious ecological problems. The lower Cenomanian aquifer containing the U deposit was mainly afflicted. Total salinity of the Cenomanian solutions reaches up to 80 g/l. Overflow of the highly contaminated Cenomanian groundwater to the Turonian collector endangers the sources of drinking water in Northern Bohemia. Our study was focused on analyzing the microbial communities and their nitrate and sulfate reduction potential regarding developing of appropriate bioremediation strategies in the region. Numerical ecology tools were applied for correlating of 16S rRNA gene denatured gradient gel electrophoresis phylogenetic profiles with environmental variables and for selecting of water habitats for further sequencing analysis of 16S rRNA genes, and functional genes for sulfate reduction – aprA, and denitrification – nirS. Significant differences were found between the microbial compositions of the two groundwater collectors. Marker genes for dissimilative reduction of nitrates were detected in waters with pH > 7. Cenomanian waters were characterized by higher diversity and distinct phylogenetic composition of denitrifying bacteria. Regardless the acidic conditions and low bacterial density - 2.7x102 to 5.3x103 cells.ml-1, three aprA gene polymorphs for the -subunit of adenosine-5’-phosphosulfate reductase were identified in the Cenomanian aquatic samples representing the highly polluted groundwaters of Bohemian Cretaceous basin. The prevalent gene variants found in the most contaminated sample C29 (41.9 g/l sulfuric acid, pH 1.68) were affiliated with the obligate chemolithoautotrophic and relevant to in situ bioremediation Thiobacillus and Desulfovibrio spp. The biocatalytic potential of the present extremophile bacteria will be used in development of pilot sulfate-reducing passive bioreactors based on the experience from acid mine drainage treatment.