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 × 10⁶ m³ 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.