The floating island system exploits the combination of aquatic plants, microorganisms, and extracellular enzymes to purify wastewater. We investigated the purification efficiency of eight aquatic plant species cultured in wastewater. The relationships of plant purification capacity with extracellular enzyme activity and microbial community were analyzed to explore the crucial factors that affect the plant purification capacity and the mechanism of pollutants removal in different plant systems. Three plant species, namely Oenanthe javanica, Thalia dealbata, and lris pseudacorus, were most effective for purification of ammonium-nitrogen (NH₄+-N), total phosphate (TP), and chemical oxygen demand (COD) with maximum efficiencies of 76.09, 85.87, and 89.10%, respectively. Urease, alkaline phosphatase (AP), and β-glucosidase activities were significantly and positively correlated with root system development (P < 0.05). Activities of urease and AP were positively correlated with NH₄+-N and TP removal, respectively. The magnitude of urease and AP activity was generally consistent with the plant’s capacity to remove NH₄+-N and TP. β-Glucosidase activity and COD removal were not significantly correlated. The dominant microbial phylum in each species treatment was Proteobacteria. Alphaproteobacteria and Bacteroidia showed > 1% relative abundance and greater involvement in degradation of pollutants in the experimental system.