Spatio-temporal distribution, taxonomic structure as well as the abundance of sulfate-reducing bacteria and the total prokaryotic communities were investigated by Sanger's and next-generation 16S rRNA gene sequencing and quantitative polymerase chain reaction in the chemocline, monimolimnion and sediment of Rogoznica Lake. Distribution of these communities is consistent with physico-chemical partitioning. Clear vertical distribution of microbial communities with family Chomatiaceae dominating the chemocline, class Deltaproteobacteria and phylum Bacteroidetes dominating the monimolimnion with significantly more abundant archaeal populations in sediment, was revealed during the stratification. Their structure and the abundance during the investigated seasons was stable, however, seasonal changes were observed at lower taxonomic levels within sulfate-reducing bacteria. During the winter conditions Desulfovibrio/Desulfomicrobium (DSV) phylogenetic subgroup dominates, while during the summer Desulfococcus/Desulfonema/Desulfosarcina (DCC) subgroup, which is characteristic for the sediment, is more abundant. Holomictic conditions led to an almost complete change in the structure of the prokaryotic communities in the water column of the lake. Chromatiaceae were replaced by Thioglobaceae family (SUP05 cluster), while the abundance of Planctomycetacia and Chlorobia increased, and phylum Epsilonbacteraeota, which was not detected during the stratification, appeared. Low number of identified dominant groups underpins the carbon, nitrogen and sulfur cycle. In contrast to holomictic conditions, no potentially nitrifying nor denitrifying bacteria were found during stratification, while the potential for anammox was very weak. Also, in a stratified conditions, a large proportion of unclassified bacteria was detected, especially in the sediment. Their physiology and ecological role in the lake remains unknown, indicating the need for further investigation of their morphological and functional characteristics.