In this study, we investigated the adsorption of heavy metals Cu²⁺, Cd²⁺ and Ni²⁺ by natural Microcystis bloom biomass in different concentrations and different pH levels. The results showed that when the heavy metal concentrations were 20.00, 60.00, 100.00 and 140.00 μg/ml, the removal efficiencies (REs) of Cu²⁺ were 67.79%, 37.47%, 35.93% and 34.70%, respectively, adsorbed by 150 mg dry weight Microcystis bloom. REs of Cd²⁺ were 73.31%, 65.87%, 60.09% and 42.37%, and REs of Ni²⁺ were 47.89%, 31.87%, 28.46% and 21.61%, respectively. At the lower metal concentration level of 20.00 μg/ml, REs of three heavy metals were the highest. A higher initial metal ion concentration resulted in a higher adsorption capability based on per gram biomass. REs of three metals was Cd²⁺ > Cu²⁺ > Ni²⁺ at the same metal concentration level. The optimum pH level for the adsorptions of Cu²⁺, Cd²⁺ and Ni²⁺ were 5.0, 6.0 and 6.0, respectively. The highest REs at the optimal pH level reached 71.90%, 85.67% and 55.43% for Cu²⁺, Cd²⁺ and Ni²⁺ in 20.00 μg/ml metals, respectively. The soluble substances released from Microcystis cells had little influence on the REs. Our results showed that the Microcystis bloom could be used as an effective adsorbent material to remove toxic heavy metals from wastewater.