The reduction in open-channel flow velocity due to China’s South-to-North Water Diversion Project (SNP) increases the risk of benthic algal community blooms resulting in drinking water safety issues. Consequently, it has attracted attention from all walks of life. However, regulatory measures to mitigate the risk of algal blooms and the main risk-causing factors are unclear. This study simulated the river ecosystem of the SNP channel through water diversion. Simulated gradient-increasing river flow velocity affects environmental factors and benthic algal alterations, and can be used to explore the feasibility of regulating the flow velocity to reduce the risk of algal blooms. We found that the algal biomasses in the velocity environments of 0.211 and 0.418 m/s decreased by 30.19% and 39.88%, respectively. Community structure alterations from diatoms to filamentous green algae were 75.56% and 87.53%, respectively. We observed significant differences in biodiversity, especially in terms of richness and evenness. The α diversity index of a species is influenced by physical and chemical environmental factors (especially flow velocity). Our study revealed that flow velocity is the main factor affecting the growth and outbreak of benthic algae. The risk of algal blooms in open channels can be effectively mitigated by regulating the flow velocity. This provides a theoretical basis for ensuring the water safety of large-scale water conservancy projects.