In this work, a reliable understanding of the storage patterns and flow dynamics of a tectonically complex karst system is attained by means of the combined analysis of results derived from geological and karst-specific -i.e. hydrogeological- approaches (hydrodynamic, hydrochemical, hydrothermal and isotopic). The pilot site comprises rocks belonging to six different complexes within the Betic Cordillera: External Zone (1), Flysch Complex (1) and the Internal Zone (4). Quick and sharp variations in natural responses after rainfall were recorded in the overflow springs located in the External Zone. In contrast, groundwater drained by permanent springs placed in the Internal Zone present high mineralization and temperature values, as well as lagged and buffered responses to precipitation events. At a first glance, one could assume that two independent systems with different behaviors are at work, following a classical interpretation: conduit flow-type functioning for Jurassic limestones (External Zone) and diffuse-flow behavior for the Triassic calcareous rocks (Internal Zone). However, integration of results with those derived from the water budget and geological observations leads us to propose a sole aquifer, formed by rocks belonging to several geological domains, but hydrogeologically connected, where shorter and longer water–rock interactions along flow paths coexist. Overthrust surfaces and the subsequent normal faults involve diverse low permeable formations imbricated within a tectonic suture, inducing strong heterogeneities in groundwater flow patterns. The geological complexity and the inner geometry at the southeast border of the aquifer jointly modulate the global signal coming from the External Zone, which is attenuated before arriving at the permanent springs found in the Internal Zone. We conclude by emphasizing that a continuous transfer of feedback from geological to hydrogeological approaches, and vice versa, enhances knowledge in both directions, helping us to avoid misinterpretations about the hydrogeological behaviors of aquifers and, ultimately, to better evaluate and manage water resources.