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While clay and silt matrices of gravel-bed rivers have received attention from ecologists concerned variously with the deteriorating environments of benthic and hyporheic organisms, their impact on sediment entrainment and transport has been explored less. A recent increase of such a matrix in the bed of Nahal Eshtemoa, an ephemeral river of the northern Negev, has more than doubled the boundary shear stress needed to initiate bedload, from 7 N m-2 (*=0.027) during the flash floods of 19912001 to 15 N m-2 (*=0.059) during those of 20082009. The relation between bedload flux and boundary shear stress continues to be well-defined, but it is displaced. The matrix now contains a significant amount of silt and clay size material. The reasons for the increased entrainment threshold of bedload are explored. Large-scale laser scanning of the dry bed reveals a reduction in grain-scale morphological roughness, while artificial in situ tests of matrix integrity indicate considerable cohesion. The implications for adopting bed material sampling strategies that account for matrix development are assessed. Copyright (c) 2012 John Wiley & Sons, Ltd.