To obtain sustainable aquaculture, developing appropriate treatment processes for wastewater is essential. In this study, two three-stage hybrid wetland systems were configured to treat aquaculture effluent. The two systems added with or without artificial aeration were operated under a high HLR (8.0 m/day) with a short retention time (0.96 h). By the results, COD could be effectively removed by both the systems, and it had been significantly enhanced by continuous aeration (air:water ratio being 7.5:1). For nitrogen (N) compounds, NH₄⁺-N concentration of outflow compared to the inflow was elevated in most cases under the nonaerated condition, but an opposite trend was observed for the aerated state, which indicated that dissolved oxygen (DO) required for nitrification in the natural bed was more insufficient at the high organic loading rate. TN mass removal was efficient without aeration, but it significantly declined after enhancement, possibly due to the resuspension of trapped organic N promoted by the strong airflow. The artificial aeration also significantly improved the treatment performance on phosphorus. By canonical correspondence analysis (CCA), the first-order removal rate constants of various pollutants were significantly correlated to the measured environment of the inflow. Under the high constant HLR accompanied by low DO, pollutant loading rate became the first dependent factor on removal rate for such a rapid filtration system.