There is little known about the wastewater treatment plant (WWTP) effluent microbiome, its structure and dynamics. Here, we provide a study of the microbiome of effluent leaving conventional WWTPs and entering the water environment. DNA was extracted from WWTP effluent samples collected in 2015 and 2016. The bacterial communities were studied using Illumina MiSeq 16S rRNA gene amplicon sequencing and analysed using Calypso software. The Proteobacteria, Bacteroides, Actinobacteria, Firmicutes, Tenericutes and Verrucomicrobia phyla dominated the microbiomes. The bacterial community composition at high taxonomic levels is consistent between the tested WWTP effluents, and in agreement with previous studies of WWTP effluents in different global locations. The analysed microbiomes of the WWTPs shared high similarities with human faecal microbiome and contained potential human pathogens. The bacterial phyla/class composition of the bacterial communities varied greatly in both WWTP effluents in October 2015. The bacterial diversity was slightly different between studied WWTPs. Two main bacterial clusters were detected in all samples during all sampling periods. In conclusion, this work highlights the need for a better understanding of the bacterial communities in WWTP effluent. This data should be considered when analysing the risk posed by WWTP effluent to the environment and to human health.