So I took a long look at the trello page and couldn't see any plan to allow any kind of fortifying rivers?
I'm not sure what you mean by fortifying rivers.
Like allowing a type of wall to be built on them as a river is running straight through one of my settlements and it allows masklings to enter through it
Ah , I could see something like that being handy. But there's currently no support for allowing some structures to be built over shallow water, and not others. I'll need something like that for docks and boats, so it's a possibility post 1.4.