The hydraulic and hydrogeological features of the Caposele aquifer have been investigated by using a numerical groundwater flow model. In particular, groundwater flow simulations were performed for a multilayered, unconfined aquifer in steady-state conditions for different thicknesses of the aquifer’s saturated zone. The Caposele groundwater model was carried out starting from a generic model drained by a unique spring outlet in accordance with the geo-hydrological features of the study area. The conceptual model was built considering hydrogeological features of spring catchment, and was then implemented with the MODFLOW numerical code. A combined 2D-3D approach was adopted, and the model was calibrated on borehole data available for the time period 2012–2019. Different thicknesses of the aquifer were set, and a reliable relationship was found between the hydraulic head, saturated zone and hydraulic conductivity of the aquifer. Using the MODPATH package, the mean travel time (Darcian) of groundwater was computed for five different scenarios, corresponding to the model’s depths; the analysis that was performed shows that the travel time is higher for a greater and lower for a smaller thickness of the aquifer’s saturated zone, respectively. The Caposele aquifer model was zoned in different sectors, named flow pipe areas, that play different roles in groundwater recharge-discharge processes. A vector analysis was also carried out in order to highlight the ascendant flow near the spring zone.