Fluid-mediated transport can play a key role in determining patterns of distribution and abundance for many benthic invertebrates. One critical challenge in understanding this process is to determine how flow patterns affect larval settlement, especially in those benthic environments where near-bed flows interact with irregular bed topography to create complex variations in habitat suitability and settlement probability. Boundary-layer separation over topographical projections on an irregular bed can create two distinct regions of near-bed flow (i.e., accelerating flow over the forebody and a zone dominated by slower eddies over the aftbody) that may have different effects on larval settlement. We manipulated the flow over a convex roughness element (i.e., hemicylinder) in a flume and examined how the settlement of larvae of the black fly Simulium tribulatum varied with changes in near-bed velocity and location over the substrate. Larval settlement rate was standardised to correct for variations in larval supply (i.e., among-trial differences in the concentration of larvae in suspension). Our analyses showed that position on the hemicylinder and near-bed velocity both affected settlement rate, with a strong interaction effect. In particular, the observed relationship between settlement rate and velocity was negative on the substrate's forebody and positive on the aftbody. We explore these results by considering potential physical and behavioural mechanisms affecting larval settlement. The presence of a positive relationship between flow and settlement rate in the aftbody may allow settlement on bed elements in habitat where preferred fast-flow conditions are present, but where settlement would otherwise by hydrodynamically limited. Thus, greater attention to settlement mechanisms in more realistic, topographically complex environments can not only help explain distribution patterns within substrates, but also among substrates and across habitats.