Perhaps it would be a good idea to add ports so that we can automate the transportation of materials over large bodies of water. I probably need to be placed in a specific way, which you could set up using vanilla landfill.

Currently we can load and unload cargo directly from ship, but it will be much harder to add automatic path-finding for ships as it doesn't seems like a vanilla feature. I'll take a look if there's some convient way to solve it, but..I can't guarantee I can acheive that soon enough :(

Maybe it would be possible to add ports. These should ideally be connected to the network. An automated route finding from port to port would of course be great, but for the beginning a kind of hand-placed "invisible water rail" would be an idea.

You mean...restrict ships only run over invisible rails and act like train? That might be possible, i'll have a try.

perhaps you could have ships find the fastest path to the next port using modified biter AI

You could contact https://mods.factorio.com/mod/Helicopters dev or use his code. He has a feature that allows you to send a helicopter to any specific helipad using the onscreen remote. Granted there would have to be additional checks since the port has to be in the same lake and have an accessible route, but hopefully that helps.

Invisible rails not working currently, as devs not support custom rail catogories at this moment. I've left a post on Helicopter mod and hope he can support ships.

perhaps aai's path finding may work, I've tested it out and the path finding work so if you manage to have ports that will automatically call the ship there then there is no problem

I'm not familar with AAI programmable vehicles.. can you give an example save that shows how to program the boats basically?

I apologize if I'm not accurate, but as I understand it it looks like AAI selects the vehcical that wants to be moved, then it wold find the next location (provided by the player) using a form of biter AI to get from that location to the other.