For the removal of nutrients from eutrophic stream water polluted by non-point sources, an artificial aquatic food web (AAFW) system comprising processes of phytoplankton growth and Daphnia magna grazing was developed. The AAFW system was a continuous-flow system constructed with one storage basin of 3 m³ capacity, one phytoplankton tank of 3 m³ capacity, and one zooplankton growth chamber of 1.5 m³ capacity. The system was optimized by setting hydraulic retention time of phytoplankton tank as 3 days and D. magna density as 740-1000 individual l⁻¹. When the system was operated on eutrophic stream water that was delivering 471 g of total nitrogen (TN) and 29 g of total phosphorus (TP) loadings for 45 days, 250 g (53%) of TN and 16 g (54%) of TP were removed from the water during its passage through the phytoplankton tank. In addition, 64 g (14%) of TN and 4 g (13%) of TP were removed from the water by harvesting zooplankton biomass in the zooplankton growth chamber, resulting in significant overall removal rates of TN (69%), nitrate (78%), TP (73%), and dissolved inorganic phosphorus (94%). While the removal efficiency of the AAFW system is comparable to those of other ecotechnologies such as constructed wetlands, its operation is less limited by the availability of space or seasonal shift of temperature. Therefore, it was concluded that AAFW system is a highly efficient, flexible system for reducing nutrient levels in tributary streams and hence nutrient loading to large aquatic systems receiving the stream water.