The occurrence and severity of harmful cyanobacterial or blue-green algal blooms (HABs) have increased in recent decades, posing a serious threat of illness to humans. In some countries, water contaminated with cyanotoxins that is used for drinking or haemodialysis has posed a particularly serious risk. However, it is now recognized that recreational exposure to natural toxins by skin contact, accidental swallowing of water or inhalation can also cause a wide range of acute or chronic illnesses. In this review, we focus on the importance of cyanotoxin management in recreational waters. The symptoms related with HAB poisonings, the recommended safety concentrations limit for cyanobacteria and cyanotoxins in such waters, as well as early health hazard indicators of their presence and their monitoring are all discussed. We also present in this review an overview of the methods developed in recent decades for eliminating cyanobacteria and the toxic compounds that they produce.