Weather systems that produced recharge to the aquifers in the Atacama Desert between 24.5 and 25.5°S were investigated using δ 18 O and δ 2 H data in groundwater and precipitation combined with remote sensing methods. Atmospheric systems that produced rain and snow from 1984 to 2017 were analysed using isotopic data for precipitation from the literature and this investigation. δ 18 O-lapse rates on a west to east transect for a series of precipitation events ranged from −5.0 to −1.1 ‰/km, which is similar to the global average. Groundwater stable isotopes plotted against the average elevation of the catchment basin for each spring or well sampled produce a lapse rate identical to precipitation isotopes but are enriched in δ 18 O relative to δ 2 H due to the effects of evaporation before water enters the groundwater system. Data show a seasonal cycle in the isotopic composition of precipitation, as does δ 2 H data obtained from Tropospheric Emission Spectrometer (TES) on-board the Aura satellite. These analyses demonstrate that an important source of moisture is the Pacific Ocean. Although usually discounted in climate and paleoclimate analyses of northern Chile, this source of moisture is consistent with two features of the regional land-atmosphere system. First, the hyper-arid core of the Atacama Desert at these latitudes lies in a secondary rain shadow created by the Cordillera de Domeyko which exceeds 4000 m a.s.l., which blocks further westward passage of moisture that might have crossed from the east over the Andes. Second, the weather events responsible for precipitation between 2000 and 2018 are distributed between winter systems which initiate from the south, and exceptional events at other times of the year in which moisture originates from the tropics. Particle tracking indicates that air masses resided between 10 and 30°S over the Pacific at least 4 days prior to weather events which produced rain, or snow that persisted on the ground for more than one month between 2000 and 2018, even though the triggers for these events originated in higher latitudes. Pacific moisture sources need to be better accounted for in paleoclimate studies and groundwater resources evaluation. • Precipitation collected in the southern part of the Atacama Desert is isotopically characterized. • Seasonal patterns are found in the isotope composition of precipitation and atmospheric water vapor. • Isotope data indicate moisture is derived from the Pacific Ocean, and is confirmed from particle tracking. • Groundwater isotope data indicates moisture has been derived from the Pacific Ocean on millennial timescales.