The effects of barriers to migration by adult salmon smolt have been well studied, but effects to migration of juvenile salmon during freshwater residency have not been evaluated thoroughly. We tested for differences in the relative abundance of juvenile Pacific salmon upstream and downstream of road-crossing culverts in 10 streams, 5 with moderate (upland) and 5 with low (wetland) slope. We compared stream width, bed slope, and substrate in natural channels and culverts; measured culvert water velocity during base flow; and obtained maximum and minimum culvert velocities using the flow time of dissolved solutes. We compared flow velocities to swimming speeds of rearing juvenile salmon to evaluate potential passage of fish through culverts. In upland streams with spawning adults, catch-per-unit-trap (CPUT) of juvenile coho salmon was often 2 to 3× greater above than below culverts. In these reaches, downstream migration of salmon fry from spawning locations may be limited by culvert flow velocities that exceed burst swimming speeds of juveniles. Where 2 upland crossing structures were replaced with culverts that replicated natural channel slopes, widths, and substrate, flow velocities decreased and differences in coho salmon CPUT were eliminated. In wetland streams with adult spawning reduced or absent above the crossing, CPUT of juveniles was greater below than above culverts where the outlet was perched. Thus, culverts can influence upstream and downstream fish movement and altered the distribution of rearing fish within streams.