Water is a fundamental resource for Chile’s productive structure, which is more important in arid areas, and especially with agricultural uses. This study was based on two basins (Cogotí and Illapel) located in the Coquimbo Region of north-central Chile. In this region, surface water rights were closed in 2002 and the only current option is the use of groundwater. These basins have high water demands due to the use of surface and groundwater for agricultural purposes, a fact that should influence the sustainability of groundwater reserves over time. The objective of this study was to determine how much agricultural use has affected the availability of groundwater in two basins. Under the previous context, the evolution of agricultural irrigation surfaces was evaluated using Landsat images and forest classifications. Similarly, groundwater reserves were evaluated using the recessive curves of hydrographs associated with the beginning of each hydrological year. The results show an increase in the agricultural area between 1996 and 2016, with a subsequent decrease, while groundwater reserves denoted significant decreases over time. In conclusion, a significant decrease in the volumes of groundwater reserves in both basins was observed, a decrease that is consistent with the increase in irrigated areas.