Alternative methods for monitoring the microbiological contamination of pharmaceutical water have been demanded for many years and various technologies are now on the market. Each method has specific advantages and disadvantages. In this presentation, we will show an example of the use of flow cytometry as a microbiological monitoring tool for pharmaceutical water. Continuous monitoring allows trend rules to be applied to the process data. This allows limits to be defined that allow a quick and exact reaction to possible contamination. The quality of the measured values is crucial for the use as In Process Control. Flow cytometry stands out among the alternative methods due to its very high specificity for living cells.