How is Richmond's city laid out? Did someone get confused between a Highway and a Bridge?
First of, this is a minor inconvenience that I didn't even notice on my first playthrough. That being said though, How is there water underneath the highway? It's submerging buildings that are close to Richmond. None of this makes much sense. I can only assume someone described the Highway as a bridge and then assumed that the bridge must be over water when designing this scene.
To rectify this, let's make up some scenarios where this might be probable:
Maybe this area is in lower ground than Richmond and the Water Tower. A River bank flooded, submerging the lower buildings. When The New Frontier are expanding, they specifically expand in the opposite direction to keep away from the flooded area. If we use the map from Episode 3 this would mean the Water Tower is to the south of Richmond.
The fact that New Frontier put their construction vehicles at the water tower does ruin this idea though.