Cyanotoxins in our environment threaten the integrity of aquatic ecosystems and human health. As climate change is suspected to favour cyanobacterial blooms, it is important to have an up-to-date picture of our knowledge concerning this subject. This review summarizes the effects of various environmental factors on the production and degradation of cyanotoxins, and on the detoxification of the water column in freshwater and brackish ecosystems in Quebec (Canada). The influence of some factors discussed in this paper is well known (e.g., nutrients, light, water temperature and bacterial activity), while that of others, which are equally important (e.g., salinity, wind, trace metals, pesticides and sediments), would benefit from further study.