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Water resources management in Maui, Hawaii, remains a challenge due to uneven distribution of rainfall, water scarcity in populated areas, and an ill-defined hydrological system. Based on data collected in June 2014, Niu et al. (2017) suggested that noble gases in this rapid groundwater infiltration system record seasonality and may shed light on water sources, recharge locations, and groundwater flow paths. This study goes one step further by analyzing rainwater, basal and perched (springs) aquifer data collected in June 2014 and February 2016. It shows for the first time that both rain and spring water display sharp temporal variations which are related to either seasonal (summer/winter) variations or to the strong 2015–2016 El Niño year. These spring water temporal variations also suggest that perched aquifer groundwater is extremely young and likely unreliable as a long-term water supplier. In contrast, noble gas temporal variations are absent in the basal aquifer. This, in turn, is consistent with tritium derived groundwater ages on the order of a few decades for the basal aquifer. This study further demonstrates that Ne is an excellent candidate to estimate the source elevation of rain and thus, to distinguish between orographic and synoptic-scale rain. Water stable isotope data are also presented for both years with 2016 samples exhibiting greater deuterium excesses than those of 2014, an observation consistent with the drier 2015–2016 El Niño climate. Estimated water source elevations based on δ18O for rainwater display a positive correlation with those based on Ne concentrations. • Both rain and spring water display sharp noble gas temporal variations. • Perched aquifers are very young and likely unreliable as a long-term water supplier. • Ne is an excellent candidate to distinguish orographic rain from synoptic-scale rain. [ABSTRACT FROM AUTHOR]