A flow regime can be broadly categorised as perennial, intermittent, or ephemeral. Different conceptual models are needed to capture the behaviour of these different flow regimes, which reflect the differences in stream-groundwater hydrologic connectivity. As the hydrologic connectivity becomes more transient and a catchment’s runoff response more non-linear, such as for intermittent streams, the need for explicit representation of the groundwater increases. In the present study, we investigate the connection between Northern Etna Groundwater system and the Alcantara River Basin in Sicily. To this end, we apply a modified version of IHACRES rainfall-runoff model, whose input data are continuous series of concurrent daily streamflow, rainfall and temperature data. The structure of the model includes three different modules: (1) a non linear loss module that transforms precipitation to effective rainfall by considering the influence of temperature; (2) a linear module based on the classical convolution between effective rainfall and the unit hydrograph able to simulate the quick component of the runoff; and (3) another non linear modules that simulates the slow component of the runoff and that feeds the groundwater storage. From the sum of the quick and the slow components (except for groundwater losses, representing the aquifer recharge), the total streamflow is derived. This model structure is applied separately to sub-basins showing different hydrology and land use. The model is calibrated at Mojo cross section, where daily streamflow data are available. Point rainfall and temperature data are spatially averaged with respect to the considered sub-basins. Model calibration and validation are carried out for the period 1981-1984 and 1985-1988 respectively. Furthermore, the uncertainty of model parameters is analyzed by using Monte Carlo simulation.