Addressing the threat of harmful cyanobacterial blooms (CyanoHABs) and their associated microcystins (MCs) is crucial for global drinking water safety. In this review, we comprehensively analyze and compares the physical, chemical, and biological methods and genetic engineering for MCs degradation in aquatic environments. Physical methods, such as UV treatments and photocatalytic reactions, have a high efficiency in breaking down MCs, with the potential for further enhancement in performance and reduction of hazardous byproducts. Chemical treatments using chlorine dioxide and potassium permanganate can reduce MC levels but require careful dosage management to avoid toxic by-products and protect aquatic ecosystems. Biological methods, including microbial degradation and phytoremediation techniques, show promise for the biodegradation of MCs, offering reduced environmental impact and increased sustainability. Genetic engineering, such as immobilization of microcystinase A (MlrA) in Escherichia coli and its expression in Synechocystis sp., has proven effective in decomposing MCs such as MC-LR. However, challenges related to specific environmental conditions such as temperature variations, pH levels, presence of other contaminants, nutrient availability, oxygen levels, and light exposure, as well as scalability of biological systems, necessitate further exploration. We provide a comprehensive evaluation of MCs degradation techniques, delving into their practicality, assessing the environmental impacts, and scrutinizing their efficiency to offer crucial insights into the multifaceted nature of these methods in various environmental contexts. The integration of various methodologies to enhance degradation efficiency is vital in the field of water safety, underscoring the need for ongoing innovation.