The factors affecting algae cells removal by coagulation–sedimentation–filtration processes were investigated. Differring from previous studies, which mainly focused on optimizing water treatment processes to enhance algae cells removal, this study paid more attention to the effect of algae population characteristics on their removal efficiency during conventional water treatment processes. The results showed that the size, shape, surface structures and the activity of algae cells affected the algal removal efficiency. The remaining algae species in the effluent of coagulation–filtration processes were mainly micro-algae. The smaller the size of algae cells was, the lower was the removal efficiency. The special shapes of algae cells, such as ellipsoidal, bacilliform and piece, and special surface structures, such as thorns and flagellae, might have a negative impact on algae removal. Moreover, the diversity of algae species in water also affected the efficiencies of micro-algae cell removal. The more the diversity of algae species were, the higher were the algae removal efficiencies. Therefore, algae population structure is a key factor affecting the removal of algae cells, and should be considered in the selection of the proper process for algae removal and control of algae species in raw water.