Based on investigation data obtained from January to December in the enclosed Fengxian bay throughout 2015, water quality and eutrophication conditions were evaluated on the basis of organic pollution index (A) and eutrophication index (E) and the species composition, biomass as well as bioremediation abilities of benthic algae community were analyzed. The results of water quality indicate that this mariculture area has been in serious eutrophication state. Dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) complied with the Grade inferior Ⅳ and Ⅲ, respectively. The annual average values of A and E were 1.88 ±0.21 and 29.95±1.18, respectively. The results also show that the dominant species of green algae is Ulva flexuosa, accounting for 97.3%. From March to December in 2015, the biomass of U. flexuosa increased by 1497.3 tons. The average N and P contents of algae were 3.50% ± 0.02% and 0.13%±0.01% and (4354.90±46.78)kg of N and (161.75±1.74)kg of P could be removed by this seaweed. The population of U. flexuosa has certain bioremediation abilities by assimilating nutrients generated by human aquaculture activities. However, the biomass of U. flexuosa stocked on hand could not completely remove all excess nutrients. Establishing an integrated multi-trophic level system co-cultured with macroalgae showed high bioextraction efficiencies on nutrients and could balance the nutrient produced by marine aquatic animal farming in the enclosed bay.