I could be wrong, but I was sure that the Fresh Water tag also increased the likelihood of Water sites, like Air/Earth in Mountains, etc.
Though really, I must say, I find the rivers in the MapGen to be the opposite of eye candy.
They never follow province divisions, which took me a LOT of getting used to. It doesn't bother me anymore, but at first I thought they horribly marred the look of the map. Then I realized the MapGen doesn't tend to make pretty maps at all (they work and you can read them), and it's okay.
I always set rivers to ~200 or so, and when I "clean up" a randomly generated map for use, I pay close attention to what I consider sources of Fresh Water, and flag appropriately.