Few studies have examined sediment transport patterns around in-stream structures used to enhance fish habitat despite the importance of this variable in the successful design of stream restoration schemes. The objective of this study is to examine interactions between the (excavated) pool morphology, flow and sediment transport in a restored reach of the Nicolet River (Quebec, Canada). Bedload transport was investigated using passive integrated transponder (PIT) tagged particles that were followed from positions upstream of a pair of current deflectors which were designed to maintain the excavated pool downstream. Three-dimensional numerical simulations of the flow field at various flow stages (with emerged or submerged deflectors) were used to relate near-bed velocity and bed shear stress to transport patterns and to assess the impact of varying the pool location and geometry on the flow field and water surface profiles. Results show that from 2005 to 2008, of the 117 pit-tagged particles that fell in the pool, only 27 are known to have exited. None of the 30 largest rocks entering the pool escaped. Bed shear stress values simulated at high and peak flow (slightly above bankfull level) are not sufficient to move the largest rocks in the pool exit zone. Simulations also reveal a complex water surface topography when flow is above the height of deflectors, with negative water surface slope in the pool zone. When modifying the pool geometry so that the deepest zones are close to the apex of the in-stream structures instead of in the centre of the channel, both water surface slope and near-bed velocity patterns are greatly modified. Understanding the interactions between excavated pools, bedload and 3D velocity patterns around in-stream structures is essential for long-term success of fish habitat restoration projects, and using 3D models to test various designs of artificial pools is a promising approach. Copyright © 2011 John Wiley & Sons, Ltd.