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In the semi-arid Mediterranean environment, the rainfall-runoff relationships are complex because of the markedly irregular patterns in rainfall, the seasonal mismatch between evaporation and rainfall, and the spatial heterogeneity in landscape properties. Watersheds often display considerable non-linear threshold behavior, which still make runoff generation an open research question. Our objectives in this context were: to identify the primary processes of runoff generation in a small natural catchment; to test whether a physically based model, which takes into consideration only the primary processes, is able to predict spatially distributed water-table and stream discharge dynamics; and to use the hydrological model to increase our understanding of runoff generation mechanisms. The observed seasonal dynamics of soil moisture, water-table depth, and stream discharge indicated that Hortonian overland-flow was negligible and the main mechanism of runoff generation was saturated subsurface-flow. This gives rise to base-flow, controls the formation of the saturated areas, and contributes to storm-flow together with saturation overland-flow. The distributed model, with a 1D scheme for the kinematic surface-flow, a 2D sub-horizontal scheme for the saturated subsurface-flow, and ignoring the unsaturated flow, performed efficiently in years when runoff volume was high and medium, although there was a smoothing effect on the observed water-table. In dry years, small errors greatly reduced the efficiency of the model. The hydrological model has allowed to relate the runoff generation mechanisms with the land-use. The forested hillslopes, where the calibrated soil conductivity was high, were never saturated, except at the foot of the slopes, where exfiltration of saturated subsurface-flow contributed to storm-flow. Saturation overland-flow was only found near the streams, except when there were storm-flow peaks, when it also occurred on hillslopes used for pasture, where soil conductivity was low. The bedrock-soil percolation, simulated by a threshold mechanism, further increased the non-linearity of the rainfall-runoff processes. Copyright (c) 2013 John Wiley & Sons, Ltd.