Groundwater provides the most important of the water resources used in the maintenance of communities in arid and semi-arid regions. In these areas, the usage of deep wells with motorized pumps in combination with the lack of effective regulatory policies and high human population growth (increase the water demand) impact the quality of the groundwater. This is especially the case for the San José del Cabo aquifer, in Baja California Sur. In the present study the groundwater flow system is analyzed in order to recognize the impact from variations in groundwater extraction and recharge on the phreatic levels and discharge values. In order to achieve this goal, a groundwater model was generated using the MODFLOW program. Different scenarios of extraction and recharge were calculated, based on different estimations of population growth. All the scenarios result in decreasing groundwater levels. As an important result, a relationship between the phreatic level and the extraction volume was found for the middle zone of the aquifer, where an average annual decrease of 0.5 m was observed from every 5 × 10 6 m 3 additional extraction volume. This zone is up to three times more susceptible to changes in extraction values than the southern zone. As the results show, the San José del Cabo aquifer is in a fragile state where an increment in extraction is not an option without the use of remediation technics or new sources for water supply.Cabo San Lucas cities, and Ciudad del Sol [5,6]. This aquifer is considered over-exploited since 1985, and the water demand has increased since then, associated with a high rate of population increment (actually 3.8%) [5][6][7][8][9][10][11][12][13][14]. In 2018 an annual groundwater deficit of −5.9 × 10 6 m 3 was estimated for the San José del Cabo aquifer [15].The physical characteristics of the SJCB aquifer have been described by many authors, i.e., [16][17][18]. Recently the effect that climate change and anthropogenic pressures over the San José estuary (the southernmost part of the SJCB) has been studied [19]. However, the effect of the increasing population and its consequential demand for additional water resource has not been studied in the whole aquifer. The SJCB aquifer satisfies almost all the water demand that accounts for the San José del Cabo and Los Cabos region, and an increment on the extraction of water is expected in the future. Changes need to be done in the socio-environmental conditions in order to improve the sustainability in the water sector [6]. This includes water consumption, water quality, and aquifer management. The population growth rate is still high and increasing along with the groundwater extraction (although the aquifer is already over-exploited). In this study, the behavior of the water table under different scenarios of water recharge and extraction, associated with the increment of the population in the San José del Cabo region is analyzed. On the other hand, synthesizing the available data in the model will improve the hydrogeological understanding o...