Performance of pre-treating algae-laden raw water by silver carp during a non-Microcystis-dominated period (period I) and a Microcystis-dominated period (period II) was investigated in terms of algae cell concentration, total phosphorus content, chlorophyll a and phytoplankton species structure. During period I the ineffective filter-feeding for small green algae resulted in the increase of small single algae, which led to the negative removal of chlorophyll a, and when the biomass was higher, the negative was more significant. However, due to the effective filter-feeding of silver carp for Microcystis flos-aquae, the average removal efficiency exceeded 50% at all stocking biomass levels (20–120 g/m3) used in experiments during period II. Total phosphorus removal efficiencies could exceed 50% at silver carp biomass stocking levels of 60–80 g/m3 during both period I and period II. The experimental results indicated that silver carp stocking contributed to the removal of colony-forming cyanobacteria, but led to the increase of single-cell algae (mainly green algae and diatoms) during both period I and period II. The initial phytoplankton community structure and the control of nutrient level were important factors in the choice of silver carp stocking biomass when used to purify algae-loaded water.