In arid regions throughout the world, shallow phreatic aquifers feed natural oases of much higher productivity than would be expected solely from local rainfall. In South America, the presence of well‐developed Prosopis flexuosa woodlands in the Monte Desert region east of the Andes has puzzled scientists for decades. Today these woodlands provide crucial subsistence to local populations, including descendants of the indigenous Huarpes. We explore the vulnerability and importance of phreatic groundwater for the productivity of the region, comparing the contributions of local rainfall to that of remote mountain recharge that is increasingly being diverted for irrigated agriculture before it reaches the desert. We combined deep soil coring, plant measurements, direct water‐table observations, and stable‐isotopic analyses (²H and ¹⁸O) of meteoric, surface, and ground waters at three study sites across the region, comparing woodland stands, bare dunes, and surrounding shrublands. The isotopic composition of phreatic groundwaters (δ²H: −137‰ ± 5‰) closely matched the signature of water brought to the region by the Mendoza River (−137‰ ± 6‰), suggesting that mountain‐river infiltration rather than in situ rainfall deep drainage (−39‰ ± 19‰) was the dominant mechanism of recharge. Similarly, chloride mass balances determined from deep soil profiles (>6 m) suggested very low recharge rates. Vegetation in woodland ecosystems, where significant groundwater discharge losses, likely >100 mm/yr occurred, relied on regionally derived groundwater located from 6.5 to 9.5 m underground. At these locations, daily water‐table fluctuations of ∼10 mm, and stable‐isotopic measurements of plant water, indicated groundwater uptake rates of 200–300 mm/yr. Regional scaling suggests that groundwater evapotranspiration reaches 18–42 mm/yr across the landscape, accounting for 7–17% of the Mendoza River flow regionally. Our study highlights the reliance of ecosystem productivity in natural oases on Andean snowmelt, which is increasingly being diverted to one of the largest irrigated regions of the continent. Understanding the ecohydrological coupling of mountain and desert ecosystems here and elsewhere should help managers balance production agriculture and conservation of unique woodland ecosystems and the rural communities that rely on them.

Regional effects of farming on hydrology are associated mostly with irrigation. In this work, we show how rainfed agriculture can also leave large-scale imprints. The extent and speed of farming expansion across the South American plains over the past four decades provide an unprecedented case of the effects of rainfed farming on hydrology. Remote sensing analysis shows that as annual crops replaced native vegetation and pastures, floods gradually doubled their coverage, increasing their sensitivity to precipitation. Groundwater shifted from deep (12 to 6 meters) to shallow (4 to 0 meters) states, reducing drawdown levels. Field studies and simulations suggest that declining rooting depths and evapotranspiration in croplands are the causes of this hydrological transformation. These findings show the escalating flooding risks associated with rainfed agriculture expansion at subcontinental and decadal scales.

Most sedimentary plains occupied by semiarid woody ecosystems have low groundwater recharge rates and high vadose zone salt accumulation. Their cultivation has often led to drainage of water below root zone, displacement of solutes, and rising water tables, affecting, in most extreme cases, long‐term viability of agriculture. To explore this possibility in semiarid plains of South America, we characterized vadose flow using chloride data in dry forests of central Argentina, in an area that has been subject to intense deforestation and agricultural expansion during the last century. We selected five paired stands under natural dry forests and dryland agriculture (sites deforested ≥30 years ago) and sampled sediments (n = 3 boreholes) down to 6 m depth. Profiles were consistently dry and salty in forest stands with chloride inventories (0–6 m) of 150 g/m²to 9 × 10³g/m². Under cultivation 78% to 99% of the chloride stock was leached, and total water storage was ≥30% higher than in the dry forest, with soil water content close to field capacity. Estimates of groundwater recharge rates based on residual moisture flux approach (cumulative chloride versus cumulative water curves) suggested maximum values of 0.33 to 128.4 mm/yr for dry forest and agriculture, respectively. At agricultural stands recharge was also estimated using chloride front displacement, yielding minimum values ≥5.3 mm/yr. While the long‐term impact of cultivation on regional groundwater hydrology is still unclear in the region, our findings suggest that land salinization processes are possible and need careful monitoring in areas with high agricultural expansion.