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In the context of global climate change, as well as the growing anthropogenic pressure on ecosystems, in particular water, one of such promising sources of valuable substances and energy may be the excess biomass of aquatic organisms, which is intensively formed during the “blooming” of water bodies. In addition to the significant energy potential of this type of substrate, which can be realized by methanogenesis, the use of spent digestate is possible even after the completion of the enzymatic fermentation process. The problem of investigating the biochemical composition of the spent cyanobacterial substrate and its major trace element constituents was undertaken to explore the possibility of using spent cyanobacterial biomass-based digest or blue-green algae (BGA) selected from bloom sites, as well as other post-methanogenesis substrates, as a biofertilizer. The majority of biomass is represented by organic substances, and the average mineral content is 4%–6%, which is a prerequisite for the use of digestate as a biofertilizer. The existing methods of growth test and determination of phytotoxic effect, as well as preliminary studies on the use of BGA as a biofertilizer are analyzed. The presence or absence of acute toxic effect of concentrated digestate and its dilutions on living test organisms was determined. On the basis of the obtained data, the expediency and prospects of using organic digestate based on various substrates used during methanogenesis as a biofertilizer were clarified. The possibility of their application as biofertilizer has been experimentally proven by the substrate and digestate physical and chemical characteristics determination. The possibilities of BGA biomass and activated sludge from urban wastewater treatment facilities mixture methanogenesis have been estimated.