The number and diversity of groundwater bodies (GWBs) in large French administrative regions pose challenges to their monitoring and protection by regional health agencies. To overcome this obstacle, we propose, for the Auvergne-Rhône-Alpes region (about 70,000 km2), a grouping of GWBs into homogeneous groups based on the sources of variability within a large dataset of groundwater physico-chemical and bacteriological characteristics (8078 observations and 13 parameters). This grouping involved a dimensional reduction in the data hyperspace by principal component analysis (PCA) and a clustering based on the mean values of each GWB on the factorial axes. The information lost when clustering from the sample point scale to the GWB scale and then to that of the GWB group was quantified by analysis of variance and showed that grouping GWBs is accompanied by a small loss of information. A discriminant analysis confirmed the high spatial and temporal variability within the dataset, as well as the effectiveness of the proposed method for establishing homogeneous sets. Some roadmaps for more targeted monitoring of water resources were briefly proposed.