Recent work suggests fish exploit low velocity recirculation zones in the wake of baffles to take refuge from challenging hydraulic conditions during ascent through baffled culverts. Yet in situ, it is likely that sediment deposes in the lee of baffles modifying the recirculation zone. The practical implications of how sediment deposition in the wake zone may affect passage efficiency is little understood. In our study, we employed high-speed 3D fish tracking using a direct linear transformation method, time-resolved stereo particle image velocimetry, videography and telemetry techniques to test the effects of sediment deposition on passage metrics and behaviors of juvenile rainbow trout attempting passage of an experimental flume. Controlled station-holding behavior, suggestive of flow-refuging, was absent within the recirculation zones of the clear bed trial, while such behavior was noted when sediment was present. Maximum distances of ascent on initial attempts were higher and ground-speeds were on average faster within the sediment deposition condition. Our results suggest sediment blocking the recirculation zone of weir baffles modifies the flow field to the benefit of passage.