Cyanobacteria produce various toxins and are grouped according to their target organs, namely, hepatotoxins, neurotoxins, cytotoxins, and endotoxins. But among the different toxins, microcystin is the most investigated and is considered highly toxic. The recommended guidelines by WHO for microcystin is 1 mg/L for drinking and recreational water. This review aims to provide an updated information on cyanotoxin diversity, their incidence, and influencing variables. These toxins have a direct impact on drinking water quality which further affects humans and cause toxicity in certain organs or tissues, like neuro-, nephro-, and hepatotoxicity. Thus, for water quality management, to limit toxic cyanobacterial mass development and to mitigate the possible impacts of cyanobacterial toxins, it is necessary to understand the occurrence and properties of cyanobacterial toxins, as well as the exposure pathways via which the toxins pose health hazards. Many bioactive metabolites produced by the cyanobacteria are understudied and whose origin and chemistry are still less known. As a result, the review emphasizes the need for greater research into the existence of cyanotoxins in water bodies, as well as the lesser-known cyanobacterial metabolites, in order to improve the risk assessment for human exposure and water quality.