In the case of perched culverts it is sometimes possible to make them passable to fish by constructing a small fish ladder on the downstream end. It's case specific; I've seen photos of a couple examples where this method has been used successfully. As Carcassman mentioned, adding flow velocity features inside culverts reduces their hydraulic capacity. Baffles have been used with some success when the culverts were sized large enough to allow the modifications. A glaring problem is that until the Timber, Fish, & Wildlife Act of 1988, DNR routinely permitted the installation of under-sized culverts simply because small culverts cost less. As one might expect, this led to many cases of culvert blowouts and road washouts and mass wasting during flood events. It was a big deal at the time for DNR to agree to require culverts large enough to pass expected flood flows, since it saves both money and the environment in the long term.

Sg