Would be nice and maybe even possible. With a reasonable scope and on an new map! Also, I looked for the original post and could not find it.
First off, lets rule out the idea of using acctual fluid mechanics. No game has ever done this in a good way. Also, there is no rain ever in salem so there is no flow of water anywhere and all water is salt. Salt stagnant water, it is a good thing we dont need to drink.

Now without a flow of water there would be no rivers but lets ignore that for the sake of sanity and just call them rivers.
And lets for the sake of simplicity assume that all terrain in salem has an infinite hydraulic conductivity. That is water can filter through anything giving us a uniform water level. Lets say for simplicity say that level is 0 to conform to RL. With this map generator there is no significant elevation in the inland so there would still be rivers but we would not have rivers climbing hills like we have now.
So this is how I would implement it.
A change to the terrain generator that to instead of generating lakes and rivers just lower the ground level in that area and check if it is low enough to be a lake/river.
Lets decide on a uniform water surface height at which you reach groundwater. Dig deeper than that and the tile turns to shallow water.
Drop soil in water to raise the ground below. If ground is higher than ground water level, water goes away. Droped soil should not displace water, merely replace it.
This opens of for several things.
Dugout waterways of shallow or deep water.
Implement a new boat "Dredger". Very slow moving but with a huge cargo capacity.
Implement digging and dropping soil from dredgers so that people can dredge deep rivers.
Implement a new boat "Ship". A large cargo capacity vessel that cannot travel in shallow waters, perhaps with a crew minimum larger than one?
Harbors in player towns.
Then there is the issue of clay/lime/stone-pits. Since we can raise the level of a pit, the mechanic of lowering when dug is not really relevant. I suggest a new action, extract, that comes at a hefty cost in phlegm and that does not alter elvation and letting digging/dropping work as anywhere else or disallowing digging it in pits altogether.
Then again, these are all nice things but not a priority.