For assessing the safety of drinking water supplies suffering cyanobacterial blooms in their water source, a methodology is proposed which relates the performance of their current treatment train to the quality of the raw water. The approach considers that different treatment trains can remove algal toxins with different efficiency. Maximum Tolerable (MT-) values of the raw water expressed by cell counts or by biovolumes of cyanobacteria were calculated. Three MT-categories were identified by colours; high risk (red), moderate risk (yellow) and no risk (green). Two treatment facilities using a conventional (1) and polishing train (2) were assessed using this methodology. For most of the time during an algal bloom the water quality could be classified as yellow which means short term higher toxin levels in comparison to the guide line in clear water were found. However, the red classification, indicating a high risk for drinking water quality was never reached. The model proposed can be understood as supplement of the common alert level framework, ALF-concept (Chorus and Bartram, Situation Assessment, Planning and Management. London and New York: E & FN Spon. 1999; House et al., Management Strategies for Toxic Blue Green Algae: Literature Review. Australia: CRC for Water Quality and Treatment. 2004).