Endotoxins are a component of most Gram negative bacteria, and some cyanobacteria. They may be toxic to humans when inhaled or injected, but the effects are unclear when they are ingested. In fact, low concentrations may protect children against certain allergies. Data for endotoxins in Quebec waters are unavailable, hence this study mapped levels in the waters around Montreal, using two commercial test methods. The recently developed factor C method had a greater linear range and was more convenient to use than the widely used Limulus amebocyte lysate (LAL) method. Although the methods gave endotoxin values of the same order, a consistent relationship between the two could not be established. Endotoxin concentrations in the untreated waters varied from 32 to 1,188 EU/mL, comparable in the literature from pristine waters to wastewaters. Values were generally lower in the summer. Filtration is known to be partially effective at removing endotoxins, but the effects of disinfection are not well established. Accordingly, chlorination, ozonation, and ultraviolet light were tested for the destruction of endotoxins in water, at doses found during drinking water disinfection. While chlorine and ultraviolet light had minimal effects on endotoxin levels, ozone could achieve up to 60% reductions at Ct values (concentration x contact time) as low as 2.5 mg•min/L.