Tools are needed to quantitatively evaluate the efficiency of water harvesting techniques in dryland environments under a wide range of climatic and soil physical conditions. In a case study for the arid zone of Chile, a detailed water balance was calculated using a coupled surface–subsurface hydrological model (HydroGeoSphere). In a first step, the model was parameterized with detailed runoff and soil water content data collected during simulated rainfall to calibrate surface and subsurface flow processes simultaneously, using six responsive parameters identified by a global sensitivity analysis. The calibrated model accurately reproduced observed soil moisture contents (R2 = 0.92) and runoff amounts (R2 = 0.97), and represented the overflowing infiltration trench, which is a clear improvement over existing frameworks that do not consider surface-subsurface flow interactions. A comparative analysis with a natural slope demonstrated that the trench was efficient in capturing runoff under high rainfall intensities, such as the one simulated, resulting in a significant decrease (46%) of runoff. In the final section, a detailed water balance of the trench was calculated for four characteristic years with increasing precipitation. Significant differences in the water balance components were only observed for the very wet year (with a return period of 67 yr), where 64% of the potential runoff was effectively harvested and stored in the soil profile. As such, this test case shows the ability of HydroGeoSphere to adequately represent the water balance components of a runoff water harvesting technique and shows its potential to become an effective tool for optimal water harvesting design, while taking both soil physical and climatic constraints into account.