Intense agricultural activities and pollutants from different man-made sources directly pollute rural lake water. The main aim of this study is to ascertain the water purification effect of a revetment constructed of eco-bags on a rural lake located in Jidong village, Jiangsu province, China. During the test period of 22 weeks, the microbial biomass increased from 0.089 ± 0.055 × 109 to 3.83 ± 1.02 × 109 cell.cm−2. In terms of the composition ratio, Proteobacteria, Nitrospirae and Firmicutes in the eco-bags accounted for 68.7, 9.5 and 10.1%, respectively. The growth of microbial population in the eco-bags and the growth of plants in the grass belt played a major role in the removal of pollutants. The chemical oxygen demand (COD), NH3–N, total nitogen (TN), total phosphorus (TP) and total suspended solids (TSS) removal efficiencies in the lake water were 43.9, 17.9, 43, 25.9 and 74.5%, respectively, while the dissolved oxygen (DO) concentration increased from 1.85 ± 0.42 to 2.93 ± 0.46 mg.L−1 during the 22 week test period.