The abilities of three artificial substrates (solid filler, bio-cord and nylon gauze) on purifying the eutrophic waters were compared in relation to the biotic and abiotic influencing factors based on a field microcosm experiment in Meiliang Bay of Lake Taihu. The results were as follows:(1) all of the three artificial substrates could significantly reduce the water turbidity. In comparison, water turbidity of the nylon gauze treatment group decreased by 94.2%, which was the highest decrease by per unit mass substrate (36.18 NTU/g); (2) comparing with the control group, the growth of algae in all three treatment groups were significantly inhibited; (3) the removal amounts of total nitrogen and phosphorus by the artificial substrates were significantly different among the three treatment groups respectively, with a 25.55%, 10.21%, 51.54% accumulative removal of total nitrogen, and a 38.93%, 38.33%, 62.98% accumulative removal of total phosphorus for the solid filler, bio-cord and nylon gauze, respectively; and (4) substrate physicochemical characteristic, biomass and activity of periphytic algae and bacteria, substrate quantity, and the releasing of dissolved nutrients attached on substrates are the key factors affecting the abilities of artificial substrates to purify eutrophic waters. In conclusion, nylon gauze has advantages over the other two substrates with high biomass and microbial activity by per unit mass periphyton, less dissolved nutrients attached on itself, lighter weight and cheaper price. Hence we suggest that nylon gauze is an ideal artificial substrate in purifying eutrophic waters.