I use the Cape May Canal to take my boat between Delaware Bay and the Atlantic Ocean, and the waters off the ferry terminal at the Delaware Bay end of the canal are always tricky. You watch your depth gauge like a hawk and go very slowly, ready to throw the throttle into full reverse at the slightest bump.
That said, a harbor pilot ought to know this and ought to know where the ferries typically reduce the depth.
Good points on the effect of prop wash around busy docks in silty harbors.