Intense use of groundwater in urban areas requires appropriate monitoring, which in turn necessitates proper data management with employment of increasingly sophisticated statistical methods and mapping tools. An example of such an urban area with intensive use of groundwater is the study area of GeoPot Project, namely Munich (Germany) and its surroundings. The aim of the presented study was to provide a description of the hydrogeochemical characteristics of the aquifers occurring in the Quaternary and Upper Freshwater Molasse (German: Obere Süßwassermolasse – OSM) sediments and to further improve the understanding of interactions between the aquifers. The focus was put on the identification of hydrochemical facies, the chemical signatures of different water types, an understanding of occurring processes, and spatial relationships between the aquifers. In order to deal with hydrogeochemical data generated for this study, as well as with data coming from existing external databanks (e.g. BIS-BY), a methodology of quality assurance was developed. The analytical methods focused on multivariate statistics. To enhance the interpretation of the obtained clusters, a recently developed three-dimensional geological model was used for better understanding and presentation. It was found that in the study area, deeper aquifer systems represent the most distinct hydrogeochemical signature of the Na–HCO3 water type. In the remaining clusters, a transition from deeper (alkaline) to shallow (alkaline-earth) groundwater can be observed. The results of the study can be utilized for improved, sustainable groundwater management.