Abstract: In the middle channel of the South-to-North Water Diversion Project, 7 sampling sites were set up in the channel section of two hydraulic structures, Shahe aqueduct and Yellow River crossing project, including the upstream of the Shahe aqueduct, the inlet of the Shahe aqueduct, the outlet of the Shahe aqueduct, the inlet of the Yellow River crossing project, the outlet of the Yellow River crossing project, the downstream of the Yellow River crossing project, and Qinhe inverted-siphons downstream of the Yellow River crossing project, to synchronously monitor the periphytic algal communities and water quality parameters. The results showed that the dominant species of Cyanophyta were Leptolyngbya sp., Synechococcus sp., Calothrix sp., Phormidium sp., Synechocystis sp., and Chroococcidiopsis sp.. The dominant eukaryotic algal species were Desmodesmus sp., Makinoella sp., Radiococcus sp., Monactinus sp., Oocystella sp., Nitzschia sp., Synedra sp., and Ulnaria sp.. After the Shahe aqueduct, the biomass decreased by 50% and the number of algal species decreased by 16%. After the Yellow River crossing conveyance, the biomass decreased by 80% and the number of algal species decreased by 18%. After the Shahe aqueduct, the abundance of Desmodesmus sp. decreased from 26.4% to 77.4%, the abundance of Synedra sp. decreased from 10.4% to 0.4%, and the abundance of Ulnaria sp. decreased from 2.3% to 0.4%. The Yellow River crossing project reduced abundance of Leptolyngbya sp. from 82.6% to 56.5% and increased the abundance of Rivularia sp. from 6.2% to 61.8%. These results indicated that hydraulic structures significantly mediated algal communities by changing microhabitats through flow condition and water quality. This study is helpful to understand the influence of hydraulic structure on algal community.