Cyanobacteria are a group of ancient oxygenic photosynthetic prokaryotic organisms originating between three and four billion years ago. They have been reported in a wide range of environments, including oceans, lakes and rivers, as well as extreme habitats such as geothermal springs, desert soils and the Polar regions [1]. Cyanobacteria can exist as solitary, free-living cells or as colonies/filaments consisting of several to thousands of cells enclosed in mucilage. Whilst most cyanobacterial colonies/ filaments and single cyanobacteria cells are microscopic, large populations become visible as mats, crusts and blooms. Populations may be planktonic (Fig. 5.1 (a, b)), suspended in the water column, or benthic, growing on bottom substrate and sometimes forming extensive mats (Fig. 5.1 (c, d)) Extensive blooms or benthic mats of cyanobacteria can be monocultures or more commonly consist of multiple species. They have been associated with increases in nutrient concentrations (i.e. eutrophication), which has been linked to human activities such as de-forestation, agriculture and urbanization. Blooms may be catalyzed by other factors which have been linked to climate change, including increased water temperature, variations in precipitation, extended droughts and increased carbon dioxide levels (see Chapter 7). There are approximately 2000 cyanobacteria species described worldwide and more than 50 are known to have strains which produce natural compounds that are toxic (cyanotoxins). Cyanotoxins are a threat to humans when ingested (via water supplies or accidental swallowing) or from contact (dermal or inhalation). Cyanotoxins exhibit a wide range of toxicity mechanisms including: hepatotoxicity; nephrotoxicity; neurotoxicity; and dermatotoxicity [2]. Cyanotoxins can be divided into three broad groups based on chemical structures: cyclic peptides (microcystins and nodularins), alkaloids (cylindrospermopsins, saxitoxins and anatoxins) and lipopolysaccharides (LPS; Tab. 5.1).