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Rainfall and temperature variability causes changes in groundwater recharge that can also influence groundwater quality by different processes. The aim of this study is the analysis of the hydrogeochemical variations over time due to meteorological variability in two different study areas in Italy: an alluvial aquifer in the Piedmont Po plain and an alluvial-pyroclastic aquifer in the Campanian plain. The examined plains show groundwater with natural quality not satisfying the European drinking water standards, or anthropogenic contamination. The peculiar natural quality is due, in the Campanian plain, to the closeness of volcanic areas, and to the presence of reducing conditions. In Piedmont plain a test site is characterized by a point-source contamination by heavy metals, due to the presence of past industrial activities. In all the examined areas there is a diffuse nitrate contamination. The fluctuations of the ions As, F, Fe, Mn, Cr VI, NO3, and Cl were analyzed and compared, using statistical methods, with the variations over time in precipitation, temperature, and piezometric levels, sometimes significant. Results highlight the importance of the groundwater and meteorological monitoring and the key role of the recharge variation in the hydrogeochemical processes. The linking degree between rainfall/temperature variability and hydrogeochemistry is variable, in function of the typology of chemical species, their origin, and of the aquifer characteristics. The fluctuation of climate variables determines sudden changes in the geochemistry of shallow unconfined aquifers (e.g., in the Piedmont plain), while semiconfined or confined aquifers (e.g., in the Volturno-Regi Lagni plain) react with a greater delay to these variations. Moreover, natural quality is more affected by climatic variations than anthropogenic contamination, which is the result of multiple environmental and anthropic factors.