Mitigating harmful cyanobacterial blooms is a global challenge, particularly crucial for safeguarding source water. Given the limitations of current technologies for application in drinking water reservoirs, we propose an innovative strategy based on in-situ sediment resuspension (SR). This method’s effectiveness in cyanobacterial control and its potential impacts on water quality were assessed through laboratory culture experiments and further validated via field applications in five drinking water reservoirs. The results revealed that SR could significantly mitigate cyanobacterial growth, evidenced by the treated sets (removal rate: 3.82×106 cells L−1 d−1) compared to the control set (growth rate: 2.22×107 cells L−1 d−1) according to the laboratory experiments. The underlying mechanisms identified included underwater light reduction (2.38× increase in extinction coefficient) and flocculation and entrainment of cells by resuspended particles (30% reduction per operation). Additional contributions were noted in the reduction of bioavailable phosphate and remediation of anaerobic sediment characterized by increased redox potential. This facilitated the oxidation of iron, which in turn promoted the co-precipitation of phosphate (removal rate: 46 μg L−1 d−1) and inhibited its release from the sediment. The SR operation, devoid of importing extra substances, represents a safe and economical technology for controlling harmful cyanobacteria in drinking water reservoirs.