Drinking-water treatment is the last line of defence to ensure the provision of safe, clean water to consumers. Water suppliers using raw water with cyanobacteria at levels causing a cyanotoxin risk need to identify the points in the plant where either removal or release of toxins can occur, optimise the controls and minimise the risks of toxin breakthrough. More than one of the treatment options addressed is likely to be available at many treatment plants, and the more the barriers that are present, the lower the risk of cyanotoxins reaching the consumer in critical concentrations. While the coagulation process is ineffective for the removal of extracellular cyanotoxins, it is very effective in removing cell-bound cyanotoxins through the removal of the whole cyanobacterial cell. If pre-oxidation must be applied in the presence of cyanobacteria cells, the levels of oxidant should be sufficient to result in the residual required for the destruction of dissolved toxins.