The fluorescence signals emitted from phycoerythrin and phycocyanin have made them suitable for use as indicators to detect cyanotoxins such as microcystins in drinking water. A study examined the nature of the biliproteins fluorescence signals regarding their real-time character, sensitivity and the biliproteins behaviour in different treatment stages (of water) in comparison to microcystins. The fluorescence signals' real-time character was confirmed by fluorescence measurements, as they can be carried out without having to pre-concentrate the biliproteins. If the ratio of biliprotein to microcystin is above 1, the fluorescence signals can estimate very low concentrations of microcystins. A test conducted in 2009 compared the behaviour of both biliproteins and selected microcystins MC-LR and MC-RR during water treatment. The test results showed that the biliproteins have an early warning function against microcystins in conventional treatment stages that use pre-oxidation with permanganate, activated carbon and chlorination. However, the early warning function does not occur when chlorine dioxide is used as a pre-oxidant or final disinfectant. It is important for the biliprotein/toxin ratio of raw water to be known in order to use the biliproteins for control measurements in drinking water treatment.