The filters in some water treatment plants have a biofilm of bacteria which degrades and removes cyanotoxins. This natural biodegradation is a cost-effective and sustainable addition to the methods used to produce safe drinking water. This research examined the parameters controlling the process with a view to establishing biodegradation in other treatment plants. It was concluded that if filter beds with small particle sizes are seeded with degrading bacteria, an effective biofilter can form if pre-chlorination is avoided and if cyanotoxins are present in the inflowing source water.