Groundwater dependence in the Southeastern region of Brazil has increased during the last 30 years, especially to supply the rising agricultural production and multiple water uses in its growing cities. Knowledge about aquifer recharge is crucial for preventive water resource management, especially under climate change scenarios. Encompassed within the hydrogeological framework of the Parana Sedimentary Basin the Bauru Aquifer System (BAS) and the Guarani Aquifer System (GAS) are responsible for supplying water to more than 10 million inhabitants in the state of São Paulo, and recharge conditions in these aquifers have been poorly studied, despite the importance of groundwater for the state. Isotopologues of water represent a completely conservative tracer of water movement through the hydrological cycle, making possible determine the relation between climatological features and groundwater recharge. Since 2013 groundwater samples from two shallow wells (30 meters depth) and precipitation samples have been collected in two sites located in the recharge area of BAS and GAS aiming to evaluate variations in isotopic composition, and how the isotopic signal of precipitation could be transferred to groundwater through recharge. Seasonal variations in groundwater levels were modulated by local precipitation regimes, and large climatological features, such as the 2014-2016 ENSO event, which was responsible for a continuous lowering of water levels observed until 2016. Isotopic composition of precipitation in both sites presented large variation (variation on d18O up to 16‰) and were marked by strong seasonality with enriched values observed during dry season while depleted values during wet season. During most part of the year d-excess values were higher than 10‰, indicating the influence of moisture recirculation processes during air masses displacement. The calculated weighted average values for d18O in precipitation were -5.70 and -5.10‰, respectively for BAS and GAS sites. Groundwater isotopic composition presented small variations when compared to precipitation (variation on d18O less than 1.5‰). Despite small isotopic variations in groundwater, d-excess values presented large variation, and most samples positioned below the local meteoric water line, indicating the occurrence of strong evaporative processes associated to kinetic fractionation along the unsaturated zone. Average values for d18O in groundwater were -6.93 and -7.25‰, respectively for BAS and GAS sites, which were more depleted than weighted average precipitation. However, such values are similar to isotopic composition of precipitation during the wet season, when the South America Monsoon System is very active, and a large amount of vapor recycled from the Amazonian region is available in the atmosphere and is responsible for the formation of the South Atlantic Convergence Zone. These findings could shed light on past climatic conditions associated to recharge of very old groundwater (up to 500 ky) found in confined portion of GAS.