This report presents the findings from task 2.1 of the SafeCREW project, which aimed to monitor seasonal microbial quality changes in source waters of near-natural treatment systems, such as managed aquifer recharge (MAR). Two case study locations, Hamburg and Berlin, were examined to understand microbial dynamics over time. Microbial cell counts in source waters were monitored using flow cytometry (FCM), which enables the analysis of bacteria, protozoa, and viruses. In addition, organic matter in source waters and during near-natural treatment was analyzed using techniques such as Liquid Chromatography-Organic Carbon Detection (LC-OCD), fluorescence spectroscopy, and absorption measurements. These methods provided detailed insights into the type and quantity of organic substances, which influence microbial growth. Notably, biopolymers—organic substances produced during microbial degradation—were identified as indicators of microbial activity and surface water influence. By combining microbiological and organic analyses, a comprehensive monitoring system can be developed that provides extensive information not only on seasonal changes in microbial quality, but also on the underlying causes and influencing factors. This enables targeted and effective control of water treatment processes and helps to ensure high water quality.