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An image cytometer (CYT) for the analysis of phytoplankton in fresh and marine water environments is introduced. A linear quantification of the number of cells over several orders of magnitude of concentrations was observed using cultures of Tetraselmis and Nannochloropsis measured by autofluorescence of the chlorophyll in a laboratory environment. The functionality of the system outside the laboratory was analysed by phytoplankton quantification of samples taken from marine water environment (Dutch Wadden Sea, The Netherlands) and fresh water environment (Lake Ijssel, The Netherlands). The CYT was also employed to study the effects of two ballast water treatment systems (BWTS), based on chlorine electrolysis and UV sterilisation by determining the vitality of the phytoplankton. In order to ensure the detection limit, a large volume (1l) of samples was collected and concentrated to 3 ml using CelltrapTM filters. The results were compared to benchmarked flow cytometer and PAM Fluorometry at Marine Eco-Analytics (MEA-NL). The image cytometer reached a 10 cells/ml limit of detection (LoD) with an accuracy between 0.7 and 0.5 log, and a correlation of 88.29% in quantification and 96.21% in vitality, when compared to benchmarked monitoring techniques.