Unexpected changes in source water microbial quality can profoundly influence the efficacy of drinking water treatment resulting in potential risk to consumers. Within the framework of the project “Regionale Wasserversorgung Basel-Landschaft 21” we are investigating microbial dynamics in karstic springs used for drinking water production. Our aim is to assess the impact of natural events (for example rainfall) on bacterial concentrations in spring water. To this end, we combine conventional microbial methods with online monitoring technologies including in-house developed fully automated online flow cytometry. This allows for the first time the monitoring of dynamic changes in bacterial concentrations at high temporal resolution and in combination with other variables.