Phytoplankton is an important water-quality indicator due to its high species differentiation, fast growth rates and responsiveness to environmental actuators. National and regional regulations and directives call for a detailed assessment of phytoplankton blooms as an indicator of the ecological status of various types of waters. Microscopic analysis of samples takes a lot of time and, therefore, only detects low-frequency changes. Automated systems, such as scanning cytometry, can fill the gaps between microscopical examinations by gathering information on rapid, high-frequency changes and, thus, permit real-time, in-situ operational monitoring. This article discusses modern scanning flow cytometry as a practical means to obtain real-time information on changes in plankton communities in marine, coastal and estuarine waters.