When studying large multiparametric databases with very heterogeneous parameters (microbiological, chemical, and physicochemical), covering a wide and heterogeneous area, the probability of observing extreme values (Z-score > 2.5) is high. The information carried by these few samples monopolizes a large part of the information conveyed by the entire database. The study of the spatial structure of the data and the identification of the mechanisms responsible for the water quality are then strongly degraded. Data transformation can be proposed to overcome these problems. This study deals with a database of 8110 groundwater analyses (Occitanie region, France), on which the bacteriological load was measured in Escherichia coli and Enterococci, in addition to electrical conductivity, major ions, Mn, Fe, As and pH. Three modes of data conditioning were tested and compared to the treatment with raw data. The results show that log transformation is the best option, revealing a relationship between E. coli content and all the other parameters. By reducing the impact of extreme values without eliminating them, it allowed a concentration of information on the first factorial axes of the PCA, and consequently a better definition of the associated processes. The spatial structure of the principal components and their cartographic representation is improved. The conditioning of the data with the square root function led to an intermediate improvement between the logarithmic transformation and the absence of conditioning. The application of these results should allow a targeted, more efficient, and therefore, less expensive monitoring of water quality by Regional Health Agencies.