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 (τ* = 0.027) during the flash floods of 1991–2001 to 15 N m-2 (τ* = 0.059) during those of 2008–2009. 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.