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Interaction between soil pedogenesis, subsurface water dynamics, climate, vegetation and human ingenuity in a desert environment has been found to result in a unique ecohydrological system with an essentially three dimensional sedimentation structure in the bed of a recharge dam in Oman. A 3-D array of silt blocks sandwiched by dry sand-filled horizontal and vertical fractures was studied in pot experiments as a model of a natural prototype. Pots are filled with a homogenous sand-silt mixture (control) or artificially structured (smart design, SD) soil substrates. Rhodes grass and ivy (Ipomea, Convolvulaceae) were grown in the pots during the hottest season in Oman. Soil moisture content (SMC) was measured at different depths over a period of 20 days without irrigation. SD preserved the SMC of the root zone for both ivy and grass (SMC of around 25%-30% compared to < 10% for control, 3 days after the last irrigation). Even after 20 days, SMC was around 18% in the SD and 7% in the control. This, similar to the case of a natural prototype, is attributed to the higher upward capillary movement of water in control pots and intensive evaporation. The capillary barrier of sand sheaths causes discontinuity in moisture migration from the micro-pores in the silt blocks to sand pores. The blocks serve as capillarity-locked water buffers, which are depleted at a slow rate by transpiration rather than evaporation from the soil surface. This creates a unique ecosystem with a dramatic difference in vegetation between SD-pots and control pots. Consequently, the Noy-Meir edaphic factor, conceptualizing the ecological impact of 1-D vertical heterogeneity of desert soils, should be generalized to incorporate 3-D soil heterogeneity patterns. This agro-engineering control of the soil substrate and soil moisture distribution and dynamics (SMDaD) can be widely used by desert farmers as a cheap technique, with significant savings of irrigation water.