Abstract:The aim of this study was to determine the effect of flowback water on an activated sludge biocenosis during municipal wastewater treatment in the sequencing batch reactors (SBRs). Two series were performed. In series 1, only municipal wastewater was treated, whereas in series 2, municipal wastewater with pre-treated flowback water was used. Flowback water constituted 3-5% of the influent and was introduced to the SBRs twice per week. Introducing flowback water did not decrease the quality of effluent from the SBRs. However, the composition of the activated sludge biocenosis differed between series, ie the biodiversity of protozoa and the relative abundance of microfauna in functional groups changed after flowback water addition. Polymerase chain reaction -denaturing gradient gel electrophoresis (PCR-DGGE) showed that the ammonia oxidizers community responded faster to flowback water addition than the total bacterial community and remained relatively stable during treatment. However, after 9 weeks of exposure to flowback water, ammonia oxidizing bacteria (AOB) biodiversity decreased. This suggests that prolonged exposure could cause nitrification problems, leading to deterioration in effluent quality.