In this study the influence of low-temperature (8 °C), sludge retention time (SRT) and loading of spotlight wastewater micropollutants (MPs) on bacterial community of activated sludge was investigated with a special focus on nitrification. Two Sequencing batch reactors (SBR) and two membrane bioreactors (MBR) were operated with synthetic municipal-like wastewater receiving and not receiving ibuprofen, diclofenac, estrone and 17α-ethynylestradiol (EE2). Bacterial population studies were related to removal efficiencies of studied MPs. The results showed that studied bacterial communities significantly differed from all previously published nitrifying activated sludge communities. Exceptionally low concentration of autotrophic nitrifying bacteria were found (< 0.5%) as well as no common heterotrophic nitrifies were presenting in activated sludge and therefore could not be related to the MPs removal. Additionally SRT had a spacious effect on the diversity of bacteria and bacterial population shifts under pressure of MPs. Growth of Firmicutes was suppressed by presence of MPs in all the reactors. Increase of MPs concentrations in wastewater improved the removal of EE2. Abundance of Delta- and Gammaproteobacteria showed positive correlation with diclofenac removal.