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Identification of a geomorphic index to represent lower thresholds for minor flows in ephemeral, alluvial streams in arid environments is an essential step as a precursor for reliable flash flood hazard estimations and establishing flood warning systems. An index, termed Alluvial wadi Flood Incipient Geomorphologic Index (AFIG), is presented. Analysis of data from an extensive field survey in the arid ephemeral streams in southern and eastern Israel was conducted to investigate the AFIG and the control over its value across the region. During the survey we identified distinguishable flow marks in the lower parts of streams’ banks, such as niches, vegetation line, and change in bank material, which are indicative of low flows. The cross-sectional characteristics of the AFIG were studied in relationship with contributing drainage basin characteristics such as lithology, topography, and precipitation. Drainage area and hardness of the exposed lithology (presented as a basin-wide index) are the preferred descriptors to be used in estimating a specific AFIG in unsurveyed sites. Analyses of discharge records from seven hydrometric stations indicate that the recurrence interval of the determined AFIG is equal to or more frequent than 0.5 yr.