Due to increasing eutrophication of oceans and inland waters, coupled with global warming, harmful cyanobacterial blooms are on the rise. Many cyanobacterial species, as well as different strains within species, have the ability to produce toxins, posing a significant threat to aquatic ecosystems, wildlife, and human health. This chapter primarily focuses on microcystin (MC)-LR, the most common and widely studied cyanotoxin, while briefly addressing other cyanotoxins and highlighting the diverse toxicological pathways. Traditionally, risk assessments of MC-LR have centered on its hepatotoxic effects, as it is a potent inhibitor of protein phosphatases. However, recent research has highlighted estrogenicity and neurotoxicity as other crucial modes of toxicity at environmentally relevant concentrations, raising concerns about endocrine disruption and broader systemic effects. In addition to toxicological insights, this chapter places particular emphasis on the role of the gut microbiota in modulating MC-LR toxicity, shedding light on microbial degradation pathways and their potential for bioremediation. Furthermore, emerging evidence suggests that epigenetic regulatory mechanisms are influenced by MC-LR exposure, which may have long-term implications for gene expression, disease susceptibility, and transgenerational effects. Understanding these biological interactions is not only critical for assessing environmental risks but also for exploring sustainable applications. In particular, the growing understanding of cyanobacterial metabolism and microbial detoxification mechanisms opens up possibilities to utilize protein-rich cyanobacteria as an alternative feed source for farmed aquatic animals.