The consequences of physical environmental effects on embryonic survival of benthic aquatic biota remains unknown, even though this period is critical to their recruitment and population dynamics. I explored how the interaction of benthic flow and substrate roughness generated different flow regimes that affected egg displacement, survival, and therefore recruitment of a North American fish, the walleye (Sander vitreus) using a wall-jet apparatus. Roughness heights larger than walleye eggs (> 2 mm) required higher velocities to displace eggs compared to those smaller than walleye eggs (≤ 2 mm). For roughness heights larger than walleye eggs, flows that skim over roughness elements required higher velocities to displace walleye eggs compared to flows that interject between roughness elements. These results reinforce the ecological importance of heterogeneous sorting and sizing of substrate elements, which enable more sheltered pockets in the benthos that provide better microhabitats for retaining biota.