We present the latest developments in the field of microbiological monitoring of plants for the production of pharmaceutical water. With the help of online measurements, processes can be optimized, negative developments can be detected at an early stage and errors can be avoided. Various technologies for monitoring the bacterial count are available on the market. Each has its strengths and weaknesses. Flow cytometry offers decisive advantages in terms of accuracy, specificity and robustness and this is the ideal solution for bioburden monitoring for pharma water.