Display omitted •Influent wastewater changed substrate bacterial community composition seasonally.•16S rRNA, nitrification and denitrification genes were stable between seasons.•Microbial systems changed from heterotrophic state to autotrophic state.•Micro- eukaryotes were more sensitive to wastewater fluctuation than bacteria. How microbial communities respond to wastewater fluctuations is poorly understood. Full-scale surface flow constructed wetlands (SFCWs) were constructed for investigating microbial communities. Results showed that influent wastewater changed sediment bacterial community composition seasonally, indicating that a single bacterial taxonomic group had low resistance (especially, Actinobacteriota and Gammaproteobacteria). However, copy numbers of 16S rRNA, ammonia oxidizing archaea, ammonia oxidizing bacteria, nirS and nirK in the first stage SFCWs were 2.49 × 1010, 3.48 × 109, 5.76 × 106, 8.77 × 108 and 9.06 × 108 g−1 dry sediment, respectively, which remained stable between seasons. Moreover, decreases in the nitrogen concentration in wastewater, changed microbial system state from heterotrophic to autotrophic. Micro-eukaryotic communities were more sensitive to wastewater fluctuations than bacterial communities. Overall, results revealed that microbial communities responded to spatio-temporal fluctuations in wastewater through state changes and species asynchrony. This highlighted complex processes of wastewater treatment by microbial components in SFCWs.