Although the effects of periphyton on water quality and its relationship with flow conditions have been studied by researchers, our understanding about their combined action in eutrophic shallow lakes is poor. In this research, four aquatic model ecosystems with different water circulation rates and hydraulic conditions were constructed to investigate the effect of periphyton and flow condition on water quality. The concentrations of NH, TP, and chlorophyll-a and flow conditions were determined. The results show that, as a result of the rising nutrient level at the early stage and the decline in the lower limit, the presence of periphyton can make the ecosystem adaptable to a wider range of nutrients concentration. In terms of the flow condition, the circulation rate and hydraulic condition are influential factors for aquatic ecosystem. Higher circulation rate in the ecosystem, on one hand, facilitates the metabolism by accelerating nutrient cycling which is beneficial to water quality; on the other hand, high circulation rate leads to the nutrient lower limit rising which is harmful to water quality improvement. At low velocities, slight differences in hydraulic conditions, vertical velocity gradient and turbulence intensity gradient could affect the quantity of phytoplankton. Our study suggests that, considering environmental effect of periphyton, flow conditions and their combined action is essential for water quality improvement and ecological restoration in eutrophic shallow lakes.