Bank filtration and artificial recharge provide an important drinking water source to the city of Berlin. Due to the practice of water recycling through a semi-closed urban water cycle, the introduction of effluent organic matter (EfOM) and persistent trace organic pollutants in the drinking water is of potential concern. In the work reported herein, the research objectives are to study the removal of bulk and trace organics at bank filtration and artificial recharge sites and to assess important factors of influence for the Berlin area. The monthly analytical program is comprised of dissolved organic carbon (DOC), UV absorbance (UVA254), liquid chromatography with organic carbon detection (LC-OCD), differentiated adsorbable organic halogens (AOX) and single organic compound analysis of a few model compounds. More than 1 year of monitoring was conducted on observation wells located along the flowpaths of the infiltrating water at two field sites that have different characteristics regarding redox conditions, travel time, and travel distance. Two transects are highlighted: one associated with a bank filtration site dominated by anoxic/anaerobic conditions with a travel time of up to 4–5 months, and another with an artificial recharge site dominated by aerobic conditions with a travel time of up to 50 days. It was found that redox conditions and travel time significantly influence the DOC degradation kinetics and the efficiency of AOX and trace compound removal.