The structural and hydrological complexity of hard rock systems (HRSs) affects dynamics of surface–groundwater interactions. These complexities are not well described or understood by hydrogeologists because simplified analyses typically are used to study HRSs. A transient, integrated hydrologic model (IHM) GSFLOW (Groundwater and Surface water FLOW) was calibrated and post-audited using 18 years of daily groundwater head and stream discharge data to evaluate the surface–groundwater interactions in semi-arid, ∼80 km2 granitic Sardon hilly catchment in Spain characterized by shallow water table conditions, relatively low storage, dense drainage networks and frequent, high intensity rainfall. The following hydrological observations for the Sardon Catchment, and more generally for HRSs were made: (i) significant bi-directional vertical flows occur between surface water and groundwater throughout the HRSs; (ii) relatively large groundwater recharge represents 16% of precipitation (P, 562 mm.y−1) and large groundwater exfiltration (∼11% of P) results in short groundwater flow paths due to a dense network of streams, low permeability and hilly topographic relief; deep, long groundwater flow paths constitute a smaller component of the water budget (∼1% of P); quite high groundwater evapotranspiration (∼5% of P and ∼7% of total evapotranspiration); low permeability and shallow soils are the main reasons for relatively large components of Hortonian flow and interflow (15% and 11% of P, respectively); (iii) the majority of drainage from the catchment leaves as surface water; (iv) declining 18 years trend (4.44 mm.y−1) of groundwater storage; and (v) large spatio-temporal variability of water fluxes. This IHM study of HRSs provides greater understanding of these relatively unknown hydrologic systems that are widespread throughout the world and are important for water resources in many regions.