River water is an important source of Dutch drinking water. For this reason, continuous monitoring of river water quality is needed. However, comprehensive chemical analyses with high-resolution gas chromatography [GC]-mass spectrometry [MS] /liquid chromatography [LC]-MS are quite tedious and time consuming; this makes them poorly fit for routine water quality monitoring and, therefore, many pollution events are missed. Phytoplankton are highly sensitive and responsive to toxicity, which makes them highly usable for effect-based water quality monitoring. Flow cytometry can measure the optical properties of phytoplankton every hour, generating a large amount of information-rich data in one year. However, this requires chemometrics, as the resulting fingerprints need to be processed into information about abnormal phytoplankton behaviour. We developed Discriminant Analysis of Multi-Aspect CYtometry (DAMACY) to model the "normal condition" of the phytoplankton community imposed by diurnal, meteorological, and other exogenous influences. DAMACY first describes the cellular variability and distribution of phytoplankton in each measurement using principal component analysis, and then aims to find subtle differences in these phytoplankton distributions that predict normal environmental conditions. Deviations from these normal environmental conditions indicated abnormal phytoplankton behaviour that happened alongside pollution events measured with the GC/MS and LC/MS systems. Thus, our results demonstrate that flow cytometry in combination with chemometrics may be used for an automated hourly assessment of river water quality and as a near real-time early warning for detecting harmful known or unknown contaminants. Finally, both the flow cytometer and the DAMACY algorithm run completely autonomous and only requires maintenance once or twice per year. The warning system results may be uploaded automatically, so that drinking water companies may temporary stop pumping water whenever abnormal phytoplankton behaviour is detected. In the case of prolonged abnormal phytoplankton behaviour, comprehensive analysis may still be used to identify the chemical compound, its origin, and toxicity. All rights reserved, Elsevier.