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In water-limited regions, surface water and carbon fluxes are strongly controlled by soil water availability, which may be highly variable at very small spatial scales (e.g. metres) because of variations in terrain, soils, and vegetation conditions and to processes of water redistribution along hillslopes. This second of a two-part paper first evaluates the performance of a newly developed ecohydrological model over a small semi-arid experimental catchment (792ha) in southeastern Arizona. Secondly, it investigates the effects of soil properties on water subsidy resulting from lateral overland flow re-infiltration and on overall ecohydrological response. With optimized parameters, the model shows a higher ability to simulate surface energy and water fluxes than CO2 fluxes at all temporal scales. The model simulates observed CO2 fluxes fairly well at diurnal scales during the main growing seasons and the interannual variability of these fluxes in response to soil moisture variations from drought years to wet years. However, the model reproduces less well carbon assimilation in spring and positive CO2 flux pulses following early monsoon rain events, suggesting a need for further development of the model’s representations of multiple plant species and soil carbon decomposition. The model simulates soil moisture at 5cm much better than at 15cm mainly because of heterogeneous soil properties. Through five numerical experiments with varying saturated hydraulic conductivity values, it is revealed that the discharge at the outlet of this semi-arid catchment is essentially attributed to lateral overland flow that is generated mainly by infiltration-excess runoff. Subsurface flow plays a minor role in this semi-arid catchment with a very deep groundwater table (>100m). The model produces wetter soils in lowland areas along stream rills and channels through re-infiltration of lateral overland flow. This water subsidy provides plants with favourable conditions to produce more leaves, CO2, and ET fluxes in lowland areas. Re-infiltration of overland flow over complex terrain may play a role in buffering climatic impacts in a warming climate with fewer but more intense rainfall events in the Southwestern United States. Copyright (c) 2013 John Wiley & Sons, Ltd.