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Carbon sources are a critical requirement for the proliferation of algae and the occurrence of harmful algal blooms (HABs), but are often turned into methane (CH4) after the collapse of severe HABs. Here, we attempt to remove HABs, reduce algal-derived CH4 emissions, and repair the broken carbon biogeochemical cycle in aquatic systems using an integrated ecological approach including flocculation, capping, and submerged macrophyte induction, preliminary at a microcosm scale. This strategy sustainably reached 98% algal removal after 65 days of incubation and resulted in an aerobic microenvironment (ORP = +12 mv) at the sediment-water interface. The approach contributed to an approximate 60% decline in CH4 released from the aquatic environment into the atmosphere jointly through assimilation of mineralized organic carbon by submerged macrophytes, production of carbon dioxide (CO2) under aerobic conditions, and aerobic CH4 oxidation. Some of the CO2 produced in the aquatic phase contributed to inorganic carbon and formed the submerged macrophytes biomass. A combination of flocculation, capping, and submerged macrophyte incubation were significant contributors to altering the carbon budget and sealing nearly 99% of the carbon in the simulated ecosystem (the majority in sediment, followed by submerged macrophytes), providing a sustainable way to reuse algal-derived carbon and reduce CH4 emissions. (C) 2018 Elsevier B.V. All rights reserved.