Cyanobacteria are a growing concern in the province of Quebec due to recent highly publicised bloom episodes. The health risk associated with the consumption of drinking water coming from contaminated sources was unknown. A study was undertaken to evaluate treatment plants' capacity to treat cyanotoxins below the maximum recommended concentrations of 1.5 μg/L microcystin-LR (MC-LR) and the provisional concentration of 3.7 μg/L anatoxin-a, respectively. The results showed that close to 80% of the water treatment plants are presently able to treat the maximum historical concentration measured in Quebec (5.35 μg/L MC-LR equ.). An increase, due to climate change or other factors, would not represent a serious threat because chlorine, the most popular disinfectant, is effective in treating MC-LR under standard disinfection conditions. The highest concentration of anatoxin-a (2.3 μg/L) measured in natural water thus far in source water is below the current guideline for treated waters. However, higher concentrations of anatoxin-a would represent a significant challenge for the water industry as chlorine is not an efficient treatment option. The use of ozone, potassium permanganate or powder activated carbon would have to be considered.