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 by 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 COD, NH3–N, TN, TP and TSS removal efficiencies in the lake water were 43.9, 17.9, 43, 25.9 and 74.5%, respectively, while the DO concentration increased from 1.85 ± 0.42 to 2.93 ± 0.46 mg.L−1 during the 22 week test period.