There are now rivers in the wilderness, with bridges crossing them at certain points. Both are indicated on in-game maps. Characters with sufficient swimming skill may attempt to swim across the rivers.
There is now a small Wilderness Compass that appears when a character is in the wilderness to help navigate and attain bearings. The compass can be disabled via options 12.
Rivers don't actually take up any wilderness space, they're just between wilderness cells (there's no way to depict this on the ASCII map, so it looks like the river takes up that whole space, but that's actually just an approximation of where it is). His mine is still safe on dry, unflooded ground.
Looking at the placement of the river coming out of Mistral Lake and taking into account the placement of the town dock as well as the nearby abandoned caravan route heading northward, the river has been altered slightly to be south of the road leading out of Mistral Lake, rather than north of it. If that wasn't exactly clear, just examine a map in-game to see the slight change.
Also note the mountains showing up on the compass at the western and northern Edges of the World aren't really mountains. You just can't go that far yet.