A novel waterfall aeration biofilm reactor integrated with a constructed wetland (WABR-CW) system was developed to meet the challenge of decentralized wastewater treatment with a focus on nutrient removal. In a lab-scale experiment of 70 days, the WABR-CW showed a high removal efficiency for COD (85–98 %), NH4+-N (100 %), TN (60–90 %) and TP (85 %-95 %), even when different organic loading rates (OLR) were used. The CW was responsible for improving the overall performance in view of an increased nutrient removal. The CW offers denitrification capacity when the OLR is not optimal for the WABR. Based on the lab-scale experiment, a pilot-scale WABR-CW was built and tested for aquaculture wastewater treatment and reuse. A total of 63 m3 wastewater was treated of which 56.7 m3 was reused. Furthermore, the microbial structure of the WABR-CW system was investigated. A metabolic analysis highlighted the N and C metabolic pathways and functional genes distribution in the WABR-CW system. Next generation sequencing not only linked the pollutants removal performance and microbial encoding genes but also disclosed the potential ability of WABR-CW to treat more polluted and more complex wastewater. The outcomes of this study provide scale-up results and a better understanding of the functioning of the WABR-CW.