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The hydrogeochemical characteristics of the significant subterranean water body between “Cecina River and San Vincenzo” (Italy) was evaluated using multivariate statistical analysis methods, like principal component analysis and self-organizing maps (SOMs), with the objective to study the spatiotemporal relationships of the aquifer. The dataset used consisted of the chemical composition of groundwater samples collected between 2010 and 2018 at 16 wells distributed across the whole aquifer. For these wells, all major ions were determined. A self-organizing map of 4 × 8 was constructed to evaluate spatiotemporal changes in the water body. After SOM clustering, we obtained three clusters that successfully grouped all data with similar chemical characteristics. These clusters can be viewed to reflect the presence of three water types: (i) Cluster 1: low salinity/mixed waters; (ii) Cluster 2: high salinity waters; and (iii) Cluster 3: low salinity/fresh waters. Results showed that the major ions had the greater influence over the groundwater chemistry, and the difference in their concentrations allowed the definition of three clusters among the obtained SOM. Temporal changes in cluster assignment were only observed in two wells, located in areas more susceptible to changes in the water table levels, and therefore, hydrodynamic conditions. The result of the SOM clustering was also displayed using the classical hydrochemical approach of the Piper plot. It was observed that these changes were not as easily identified when the raw data were used. The spatial display of the clustering results, allowed the evaluation in a hydrogeological context in a quick and cost-effective way. Thus, our approach can be used to quickly analyze large datasets, suggest recharge areas, and recognize spatiotemporal patterns.

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