While Bay Lake is connected to Bonnet Creek, Village Lake and the Sassagoula River via canals, I don't believe *all* WDW bodies of water are fully interconnected. Most of them can (or already are) isolated.
In many places, Disney needs to have absolute control over the water levels in the waterways. That's why you'll see water levels fluctuate in Bay Lake and Seven Seas Lagoon where it's OK for it to happen, and to a lesser extent Village Lake and the Sassagoula. But with the in-park waterways they need total control of the water level.
So the water level in the Epcot/Crescent Lake/Studios waterway will always be the same level. (And while they don't really have a *need* to do it, they could conceivably build a dam at the International Gateway and empty World Showcase Lagoon. Though then you get into the issue of what do they do with the Friendships)
The Rivers of America, while connected to Seven Seas Lagoon via a canal and lock, is always kept at the same water level.
I would presume that it's the same setup with Discovery River in AK. The River might be connected to the ponds that are SE and SW of the park, but that'd be it.
There are canals/streams that run throughout the property, channeling water where it's needed within the natural and man-made waterways, but the closest those appear to come to AK is a little to the east of the park. If you could successfully portage around the various flood gates along the canals, you could conceivably paddle a small canoe from the northern service area above the MK, around through the Palm and Magnolia golf courses, down to a point about halfway between Everest and Coronado Springs, but then the aerial imagery differs from the regular map... They may have rerouted that stream/canal underground somewhere through there. (looks like there might be something that turns east toward Coronado)
Wow, I think that was about three different possible discussions all wrapped into one post.
-Rob
