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Although floods in arid environments have been documented, considerable uncertainties still exist as to the floodwater and in-channel infiltration relationships. In desert alluvial channels, the prime cause of flood discharge attenuation is water loss by infiltration into the alluvium. The present study documents flows in Nahal Zin, Israel, their infiltration into the channel bed, and the resultant change in the alluvium moisture content. The study uses a systematic combination of two experimental scales, the cross-section scale and the reach scale. Direct measurements of moisture distribution in the active channel during floods were made using time domain reflectometry. Twelve flow events were recorded. Flow patterns and their respective alluvium moisture content were analysed. A trench was dug in the alluvium for the study of alluvium properties and time domain reflectometry sensor installation. The alluvium was characterized in terms of size distribution and sediment stratigraphy, structure, and composition. Two main alluvial structures (closed and open) affected the advance of the wetting front and water losses. Alluvial units with an open structure (clast-supported) reached their maximum moisture content faster than closed structure units (matrix-supported). Small-sized particles and matrix-supported layers reduced infiltration rate. The measured velocities of the wetting front were 0.33 and 2.88mh(-1) for small and large floods respectively. The wetting front moved downward. Lateral movement was negligible. Copyright (c) 2016 John Wiley & Sons, Ltd.