Water infiltration in soils is a fundamental hydrologic process that determines the water availability for plant roots and the rate of recharge to deep groundwater bodies. When both the initial water saturation of the soil and the water infiltration rate is low, the infiltration front becomes unstable, resulting in gravity fingers that act as preferential flow channels. Preferential flow may allow for the rapid bypass of water through the evaporation zone, thereby promoting deep drainage of water into the subsoil even in arid and semi-arid regions, where the potential evapotranspiration (PET) is high and the mean annual precipitation (MAP) is low. Here, we investigate experimentally the impact of gravity fingering on deep drainage coupled with surface evaporation in a 3D porous medium. We use a cylindrical vessel packed with dry glass beads, and reproduce seasonal climatic patterns consisting of relatively short rainfall events alternating with periods of intense evaporation. We vary the volume of rainfall events and the interval between rainfall events to replicate climate conditions. We record the mass of water in the system throughout the experiment, and determine the partition between evaporation and deep drainage before and after the onset of fingering. We find that in semi-arid conditions, the fraction of water that bypasses the evaporation zone increases fourfold after gravity fingering starts. This finding has potentially important implications for understanding infiltration dynamics in arid environments and ecosystems’ response in regions susceptible to desertification.