Military has a transport ship unit that can carry land units over water. Only problem is that there's an AI bug that stops them from building the dock, the pinnacle of all naval units, but this is bypassed in Naval Scenarios, which give the CPU a dock either at the start of the game or after a certain period of time.
There's no missions though that directly require the use of the transport ship (they provide an advantage, such as using the river systems to get behind the foe, though), but I do plan to make an islands scenario that would have a more natural "earth like map" eventually, but most likely not till version 4.