Display omitted •Four pilot-scale CWs differing in plant species and planting patterns were compared.•Nutrients, antibiotics and ARGs in aquaculture wastewater were efficiently removed.•Microbial structure and diversity spatially differed in four CWs.•Treatment performances of CWs attributed to the plant physiological features. Four horizontal subsurface flow pilot-scale constructed wetlands (CWs) named as S1, S2, M1 and M2 were constructed to treat aquaculture wastewater. And two different plant species (Iris pseudacorus and Phragmites australis) were cultivated in single and mixed planting patterns in these four CWs. The removal rate of conventional pollutants (nutrient and organic compounds), antibiotics including enrofloxacin (ENR), sulfamethoxazole (SMZ), and antibiotic resistance genes (ARGs) were evaluated among those CWs. The total nitrogen and NH4+–N removal rates of all CWs were 73.24%–91.46% and 61.20%–92.27%, respectively. CWs with mixed planting patterns, such as M1 (planted with Iris pseudacorus at the forepart and Phragmites australis at the back) and M2 (alternate cultivation with Iris pseudacorus and Phragmites australis) showed better performances than CWs planted with single plant species, such as S1 (Iris pseudacorus) and S2 (Phragmites australis). However, S1 and S2 exhibited higher removal efficiencies for emerging contaminants: S1 had removal efficiencies of 77.64%, 68.70%, and 58.21% for ENR, SMZ, and total ARGs, respectively, and S2 had removal efficiencies of 81.11%, 64.94%, and 56.26% for ENR, SMZ, and total ARGs, respectively. Compared with single planting, the dominant genera in mixed planting exhibited lower relative abundance in anaerobes and higher percent of bacteria associated with nitrogen metabolism, indicating that different plant physiological characteristics affected the microbial community structures of the CWs.