In mineral-rich areas, eutrophic lakes are at risk of HMs pollution. However, few papers focused on the repair of HMs in eutrophic environment. Our study analyzed multiple forms of HMs, pore structure and microbial responses in the water-sediment system of eutrophic lake treated with biochar, Effective Microorganisms (EMs) or/ and microplastics (MPs). As biochar provided an ideal carrier for EMs, the remediation of biochar-supported EMs (BE) achieved the greatest repairment that improved the bacterial indexes and greatly decreased the most HMs in various forms across the water-sediment system, and it also reduced metal mobility, bioavailability and ecological risk. The addition of aged MPs (MP) stimulated the microbial activity and significantly reduced the HMs levels in different forms due to the adsorption of biofilms/EPS adhered on MPs, but it increased metals mobility and ecological risks. The strong adsorption and high mobility of aged MPs would increase enrichment of HMs and cause serious ecological hazards. The incorporation of BE and MP (MBE) also greatly reduced the HMs in full forms, which was primarily ascribed to the adsorption of superfluous biofilms/EPS, but it distinctly depressed the microbial activity. The single addition of biochar and EMs resulted in the inability of HMs to be adsorbed due to the preferentially adsorption of dissolved nutrients and the absence of effective carrier, respectively. In the remediation cases, the remarkable removal of HMs was principally accomplished by the adsorption of HMs with molecular weight below 100 kDa, especially 3 kDa-100 kDa, which had higher specific surfaces and abundant active matters, resulting in higher adsorption onto biofilms/EPS.