This report summarizes the work for monitoring of hydraulic residence time (HRT) carried out at the Managed Aquifer Recharge (MAR) site Berlin-Spandau waterworks. The newly installed monitoring system consists of realtime online sensor data and evaluation algorithms implemented as a web-based software tool. The combination of online data with processing tools allows time-efficient HRT evaluation. Apart from HRT estimations, the monitoring also included measurements by flow-through cytometry (FCM), meta-genomic DNA sequencing and classical microbial cultivation-based analysis. FCM cell counting allows to quantitatively detect microbial cells after staining with a DNA-binding fluorescent dye. The aim of FCM measurements was to gain insights on microbial dynamics along the flow path from the infiltration basin to the abstraction well. The FCM device was installed to measure in the infiltration basin, groundwater observation well and abstraction well in a continuously flowing sampling line that allowed for automatic and continuous monitoring in water. Microbial indicators of viruses, bacteria and protozoa were sampled and analysed by classical cultivation-based methods in parallel to the FCM measurements. The combination of FCM with cultivation-based methods aimed to establish an indicative reference cell count representing a hygienically safe water. The high-frequency flow cytometry data revealed decreasing order of total cell counts from surface water in the infiltration basin water to groundwater in the abstraction well. The fairly constant measurements in the abstraction well may allow to use FCM fingerprinting as a fast monitoring tool in combination with cultivation based methods. However, long-term measurements of FCM for at least 6 months are recommended to assess seasonal fluctuation in both source water and groundwater. Water samples were in addition characterised by DNA sequencing enabling a complete “meta genomic” analysis and taxonomic profiling including bacterial, archaea, viral, eukaryotic DNA. The DNA sequencing in combination with FCM measurements showed that total cell counts decreased along the flow path while the biodiversity increased.