The construction of large-scale water diversion projects has effectively alleviated the current situation of the uneven distribution of water resources in China. However, due to the siltation of very fine sediment and organic matter on the side wall of an open channel, and the slow velocity of the side wall flow field, it is easy for epipelic algae to be produced, which affects water quality. Because prototype observation cannot be used to predict the series of flow in real time, and the calculation of the mathematical model is affected by parameter limitations, these two methods often cannot truly reflect the hydrodynamic characteristics of an open channel with epipelic algae. Therefore, by referring to the design parameters of the water diversion project channel, this study took the epipelic algae growing on the side wall of an open channel as the research object and used the scale of 1:30 to carry out a generalized flume experiment. Through the analysis of the physical characteristics of the prototype sample, and the simulation of the cohesive force between the oblique side wall and the epipelic algae, multi-group and multi-series hydrodynamic tests were carried out. The velocity distribution law and flow field distribution law were analyzed. The research results show that the presence of epipelic algae has a certain hindering effect on the flow velocity and significantly reduces the range of the peak velocity of the channel along the water depth. The position of the maximum velocity on the vertical line of the channel flow appears at the relative water depth of 0.6. In the case of small flow, the epipelic algae group only reduces the average flow rate of the channel by 5~6%; in the case of large flow, the effect of epipelic algae on the channel flow rate is minimal. This paper includes important scientific guiding significance and practical value for the regulation of water quantity and water quality safety, as well as the protection of long-distance projects.