In vivo fluorescence methods have been accepted as a quick, simple, and useful tool for quantification of phytoplankton organisms. In this paper, we present a case study in which fluorescence methods were employed for the selective detection of potentially toxic cyanobacteria in raw water at the drinking water treatment plant. The occurrence of cyanobacteria in the drinking water reservoir and in raw water was monitored by phycocyanin fluorescence measurements and by standard methods for phytoplankton quantification (cell counts, chlorophyll a). A special attention was paid to the most critical parts of the season -- spring recruitment of cyanobacteria from sediment to water column and autumn bloom collapse. All methods showed similar patterns within the season. Phycocyanin fluorescence was found to be a simple and sensitive indicator of cyanobacteria in water and can serve as a tool that can provide an early warning about the presence of potentially toxic cyanobacterial metabolites in water.