To cope with water scarcity in drylands, stormwater is often collected in surface basins and subsequently stored in shallow aquifers via infiltration. These stormwater harvesting systems are often accompanied by high evaporation rates and hygiene problems. This is commonly a consequence of low infiltration rates, which are caused by clogging layers that form on top of the soil profile and the presence of a thick vadose zone. The present study aims to develop a conceptual solution to increase groundwater recharge rates in stormwater harvesting systems. The efficiency of vadose-zone wells and infiltration trenches is tested using analytical equations, numerical models, and sensitivity analyses. Dams built in the channel of ephemeral streams (wadis) are selected as a study case to construct the numerical simulations. The modelling demonstrated that vadose-zone wells and infiltration trenches contribute to effective bypassing of the clogging layer. By implementing these solutions, recharge begins 2250–8100% faster than via infiltration from the bed surface of the wadi reservoir. The sensitivity analysis showed that the recharge rates are especially responsive to well length and trench depth. In terms of recharge quantity, the well had the best performance; it can infiltrate up to 1642% more water than the reservoir, and between 336 and 825% more than the trench. Moreover, the well can yield the highest cumulative recharge per dollar and high recharge rates when there are limitations to the available area. The methods investigated here significantly increased recharge rates, providing practical solutions to enhance aquifer water storage in drylands.