<p>Undesirable cyanobacterial blooms in surface water are favored by eutrophic conditions and climate change will increase their prevalence. Cyanotoxins are of great concern and should be treated in water treatment plants. In this review, the possible effects of cyanotoxins and cyanobacteria to human health, and their recorded occurrence in the lakes of Greece and other Mediterranean countries, are considered. While cyanobacteria and cells may be removed by physical processes, the efficient removal of toxins, particularly those that are water-soluble, demands treatment such as reverse osmosis, activated carbon, or oxidation with ozone or chlorine with adjustment of operational parameters. Thus, due to the inefficiency of conventional systems to remove cyanotoxins from water derived from lakes, which are used as reservoirs for drinking water supply, the limitation or prevention of cyanobacterial blooms should be targeted and the role of water and environmental education is explored. In general, the findings of this paper underline the severity of cyanotoxins in water resources, the extent of their presence influenced by climate change and the necessity of the adjustment of water treatment plants to remove these threats of public health. Cyanobacteria and cyanotoxins are of great importance in the Mediterranean region since particular factors in this region can contribute to cyanobacterial blooms.</p>