Groundwater (GW) use has intensified in recent decades, threatening the ecological integrity of groundwater-dependent ecosystems (GDEs). The study of GDEs is limited; therefore, integrated, interdisciplinary environmental approaches that guarantee their monitoring and management amid current climate and anthropogenic changes are needed. A new geospatial method with an integrated and temporal approach was developed through a multicriteria approximation, taking into account expert opinion, remote sensing-GIS, and fieldwork to map groundwater-dependent ecosystem zones (GDEZ). A survey of experts (N = 26) was conducted to assign degrees of importance to the various geospatial parameters, and the mapping was carried out using 14 parameters. The reclassified parameters were normalized on a scale of 1 to 5 according to the degree of probability of the presence of GDE. The validation was carried out through fieldwork and statistical analysis. Then, the spatio-temporal changes amid changing GW levels were assessed using the summer season normalized difference vegetation index (NDVI). Two GDEZ maps were obtained, for 2002 and 2017, between which the high- and very-high-probability zones of GDEs decreased by 31,887 ha (~ 38%). The most sensitive temporal parameters that most influenced the spatio-temporal changes on GDEs were precipitation and land use, with rain exerting a slightly the greatest influence. It was also demonstrated that identified ecosystems decreased in area or were affected by aquifer depletion (NDVI-GW, r Pearson ≥0.74). This validated method allows spatio-temporal changes in GDEs to be mapped and analyzed at an annual scale and is transferable to other arid and semi-arid environments.