Abundant geomorphological, biological, and isotopic records show that Arabia repeatedly underwent significant climate-driven environmental changes during late Quaternary humid periods. Precisely mapping how the enhancement and expansion of the African Monsoon during these humid periods have affected landscape evolution and human occupation dynamics in Arabia remains a scientific challenge. Here we reconstruct an ancient water-sculpted landscape consisting of lake and river deposits, coupled with a large outlet valley in the Rub’ al Khali Desert of Saudi Arabia. During the peak of the Holocene Humid Period or before, intense rainfall reactivated alluvial floodplains and filled a ~1100 km² topographic depression, which eventually breached, carving a deep ~150 km-long valley. Coupling geologic reconstructions with transient Earth system model simulations shows that this hydrological activity was linked to higher seasonal precipitation punctuated by repeated heavy events. Analysis of lacustrine and fluvial sedimentary deposits implies sediment routing across distances of up to 1000 km from the Asir Mountains. Our results indicate that such intense flooding challenges the conventional view of simple, weak, and linear landscape stabilization following increased rainfall in Arabia. Our findings highlight the crucial role of an enhanced African Monsoon in driving rapid landscape transformations in the Arabian Desert.