Using Fish Design Flows
Normally if the culvert is at the same width as the stream and has similar material for streambed simulation the design flow issue is not considered important (Bridges, Open Arch, Embedded Pipes
For flat culverts as long as gradient less than 0.5% flow should not be an issue for increasing velocities for maximum flows.
If culverts backwatered and have adequate residual pool depth there is usually adequate depth at low minimum flows. For streambed simulation designs if there is similar bedforms inside the culvert as in the stream then no difference for fish passage.
Design flows come into play when using backwatering and also when using weir/baffle designs. Yet in most plans this is not mentioned.