Currently, human activities in ecosystems have led to adverse effects in aquifers, with the main consequences being the loss of vegetation and water availability. This paper presents a multi-criteria qualitative matrix which is developed to assign different values which estimate the potential of a specific land cover to be a groundwater recharge site. The matrix was coupled with a quantitative analysis of land cover changes in the Aguanaval aquifer, within the central zone of Zacatecas State, Mexico. Land cover changes were determined using four satellite images from 1986, 1992, 2002 and 2016. The results indicate that from 1986 to 2016 croplands and pasture increased by approximately 33,483 ha, but the most important change for croplands and pasture occurred between 2002 and 2016 with an increase of 31,607 ha; mixed forest land class occupied 16.49% in 1986, but an increase in the period from 1986 to 1992 reached 18.69% and decreased to 13.30% and 11.76% for 2002 and 2016, respectively. For the mixed rangeland covering 61.26% of the aquifer area, the major land cover in 1986 decreased substantially in 2016 reaching only 17.09% of total area. It was identified that the sites with a high recharge potential are located in the east and central-southeast and the medium recharge potential sites are located in the central part while the low potential sites are distributed to the north and southwest side of the aquifer.