Metagenomic technique was employed to characterize the seasonal dynamics of activated sludge (AS) communities in a municipal wastewater treatment plant (WWTP) over 4 years. The results indicated that contrary to Eukaryota (mainly Rotifera and Nematoda), abundances of Bacteria and Archaea (mainly Euryarchaeota) were significantly higher in winter than summer. Two-way analysis of variance and canonical correspondence analysis revealed that many functionally important genera followed strong seasonal variation patterns driven by temperature and salinity gradients; among them, two nitrifying bacteria, Nitrospira and Nitrosomonas, displayed much higher abundances in summer, whereas phosphate-removing genus Tetrasphaera, denitrifier Paracoccus and potential human faecal bacteria, i.e. Bifidobacterium, Dorea and Ruminococcus, showed significantly higher abundances in winter. Particularly, occurrence of dual variation patterns beyond explanation merely by seasonality indicated that multivariables (e.g. dissolved oxygen, sludge retention time, nutrients) participated in shaping AS community structure. However, SEED subsystems annotation showed that functional categories in AS showed no significant difference between summer and winter, indicating that compared with its microbial components, the functional profiles of AS were much more stable. Taken together, our study provides novel insights into the microbial community variations in AS and discloses their correlations with influential factors in WWTPs.