The Mangshan pumping station is one of the most important water sources in the Yellow River basin, and it has been included in the list of national drinking water sources. When water from the Yellow River is pumped, desilted, and transferred to the waterworks at the Mangshan pumping station, the aquatic biotope dramatically changes throughout these steps. To better understand how these artificial actions influence the phytoplankton by changing the biotope, the changes in phytoplankton from the river intake to the entry of the waterworks were investigated in June 2014. Overall, 7 sampling sites were set up along the path of the water. The measured water quality parameters included, among others, water temperature, dissolved oxygen, and total phosphorus, and all were monitored simultaneously. Structural changes in phytoplankton community and the relationship with the environmental factors were analyzed using two multivariate analysis techniques:Polar Ordination Analysis (POA) and Redundancy Analysis (RDA). The phytoplankton community structure, their density, and the biomass changed significantly from the river intakes to the waterworks. The phytoplankton biomass and biodiversity showed a decreasing trend along the path of the water. Furthermore, POA analyses indicated that the 7 sampling sites could be divided into three biotopes, and that these three biotopes reflected the change along the way. Finally, RDA analyses showed a significant influence of the environmental factors on the community structure, which differed from the influence these factors have in the lake and other natural water bodies.