The increasing occurrence of hepatotoxic cyanobacterial blooms in fresh waters is one of the most serious risks to human health in the 21^st century. Therefore, proper management of waters contaminated with cyanobacteria requires elaboration of the appropriate methods to remove cyanobacterial hepatotoxins-microcystins (MCs) from the environment. Many chemical and physical procedures have been proposed to remove MCs from fresh waters, but more attention is now paid to more environmentally friendly and cost-efficient techniques for MCs reduction. Therefore, this paper presents a summary of the current knowledge concerning the possible use of natural processes with the participation of environmental bacteria for MCs degradation in fresh water.