Abstract: 【Objective】The residue of enrofloxacin (ENR) in aquaculture ponds has attracted widespread concern. Submerged macrophytes are widely used in aquaculture environment restoration projects due to their effective water purification effects, environmental friendliness, and easy operation.This study was aim to investigate the individual and combined effects of ENR residue and planting Vallisneria natans on nitrogen transformation in the sediment of aquaculture ponds.【Method】 Microcosm experiment was carried out using PVC tanks.【Result】The results showed that 41.4% and 51.5% of the TN and NH4+-N concentrations in the pore water were removed by Vallisneria natans. The removal efficiencies were only 26.8% and 25.1% in the sediment with ENR residue, respectively. The rhizosphere effect of Vallisneria natans increased the abundance of bacteria, archaea, Anammox, and amoA by 111.8%, 153.3%, 127.2%, and 517.6% in the sediment, respectively. But the residue of ENR weakened the promoting effect of Vallisneria natans on the microbial community. Planting Vallisneria natans significantly increased the contents of narG, nirK, and nirS by 188.65%, 371.34%, and 210.25% in the rhizosphere sediment, respectively. ENR residue at 0.6–0.8 mg/kg in the sediment had no significant effect on the denitrification gene contents, but inhibited the leaf-length growth of Vallisneria natans significantly.【Conclusion】The growth of Vallisneria natans, its nitrogen removal capacity and promoting effect on microbial communities would be affected in the aquaculture sediment with ENR residue.