Since a riverside highway is usually several meters above the water level, an underpass offers direct access to water. An overpass, on the other hand, would need to come down steeply on the other side, which is not only inconvenient but also very ugly.

But I've heard that some species don't like to go through tunnels, because predators might lurk in the dark corners (or something like that). So the architecture will have to adapt to the species it is designed for.