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[Display omitted] • CAPM flocculation and screen filtration were effective for cyanobacteria removal. • Proteins and high molecular weight (MW) DOM were preferentially removed. • Electrostatic binding of high MW DOM and CPAM led to the formation of large flocs. • Cyanobacteria were encapsulated by the polyelectrolyte complexes of DOM and CPAM. Prompt removal of densely accumulated cyanobacteria is a straightforward method to alleviate the harm of cyanobacterial blooms to lakes. In this study, a cyanobacteria harvesting ship based on flocculation and filtration was used for the removal of cyanobacteria in a bay of Dianchi Lake (Yunnan Province, China), in which the fate and influence of lake dissolved organic matter (DOM) were investigated. After flocculation with 1–3 mg/L cationic polyacrylamide (CPAM) and filtration with the 100-µm-pore-sized screens of a rotary drum filter (RDF), >90 % of cyanobacteria was removed and the DOM was slightly reduced from 7.83 mg/L to 4.61 ∼ 6.49 mg/L. Tryptophan protein-like and high molecular weight (MW) DOM was selectively removed, increasing the humification index and decreasing the biological index in the treated water. Lake DOM, especially the high MW fractions of lake DOM, played an important role in CPAM flocculation. Cyanobacteria could not be effectively flocculated in Milli-Q water while the removal efficiency increased to over 90 % when 1–3 mg/L high MW DOM of Dianchi Lake was added. Three lakes in Yunnan Province were also plagued by cyanobacterial blooms, including Erhai Lake, Qilu Lake, and Xingyun Lake. The high MW DOM (1.7–2.7 mg/L) in the lakes could also deduce the effective flocculation of cyanobacteria with CPAM. The flocculation mechanism could function by the interactions of quaternary ammonium groups of CPAM and carboxylate groups of high MW DOM that form net-like polyelectrolyte complexes (PECs), and coexisting cyanobacteria cells were encapsulated into the PECs, leading to the formation of large flocs under stirring conditions. In the lakes with high densities of cyanobacteria, there might be enough high-MW DOM to promote the flocculation of CPAM, and after flocculation-filtration treatment, both cyanobacteria and cyanobacteria-deprived DOM were effectively removed. [ABSTRACT FROM AUTHOR]