Wadi aquifers in Saudi Arabia historically have been recharged primarily by channel loss (infiltration) during floods. Historically, seasonal groundwater levels fluctuated from land surface to about 3 m below the surface. Agricultural irrigation pumping has lowered the water table up to 35 m below the surface. The geology surrounding the fluvial system at Wadi Qidayd consists of pelitic Precambrian rocks that contribute sediments ranging in size from mud to boulders to the alluvium. Sediments within the wadi channel consist of fining upward, downstream-dipping beds, causing channel floodwaters to pass through several sediment sequences, including several mud layers, before it can reach the water table. Investigation of the wadi aquifer using field observation, geological characterization, water-level monitoring, geophysical profiles, and a hypothetical model suggests a critical water level has been reached that affects the recharge of the aquifer. The wetted front can no longer reach the water table due to the water uptake in the wetting process, downstream deflection by the clay layers, and re-emergence of water at the surface with subsequent direct and diffusive evaporative loss, and likely uptake by deep-rooted acacia trees. In many areas of the wadi system, recharge can now occur only along the channel perimeter via fractured rocks that are in direct horizontal hydraulic connection to the permeable beds above and below the water table.