The indicator function of the fluorescence signals of the cyanopigments phycocyanin and phycoerythrin as early warning parameters against the microcystins in drinking water was investigated by lab- and pilot-scale studies. The early warning function of the fluorescence signals was examined with regard to the signals' real-time character, their sensitivity and the behaviour of the cyanopigments in different treatment stages in comparison to microcystins. Fluorescence measurements confirmed the real-time character, since they can be carried out on-site without the pre-concentration of pigments. The limit of detection of phycoerythrin is determined at 0.7 microg/L and of phycocyanin at 5.3 microg/L respectively. If the pigment/microcystin ratio is known and calculated to be higher than 1, very low microcystin concentrations can be estimated by the fluorescence signals. The compared behaviour of both pigments and selected microcystins (MC-LR and MC-RR) during water treatment shows that pigments have an early warning function against microcystins in conventional treatment stages using pre-oxidation with permanganate, powdered-activated carbon and chlorination. In contrast, cyanopigments do not have an early warning function if chlorine dioxide is used as a pre-oxidant or final disinfection agent. In order to use pigment control measurements in drinking water treatment the initial pigment/toxin ratio of the raw water must be known.