I have posted this in another Zora to Rito thread...

If you take a large number of things into consideration, real life, movies, etc. then you can answer alot of these things.

First off, anyone see Water World? Based off of real world principles, at least the planet it's self, IF the water levels rose that high on earth, the fresh water (from the ice caps, or in this case, the rain) would be enough to delude the salt water, there for making it drinkable (btw, that's a scientific fact) so, even if the River Zoras didn't like salt water, there would be little to no salt in the Great Sea for them to get their fins all in a bunch.

Secondly, if we look at evolution, in real life, we, humans, evolved from fish, which turned into reptiles, which then turned into mammals, which again turned into primates, and of course finally us (scientific fact, not religion). Birds are a direct descendant of dinosaurs. And dinosaurs came from the waters as fish. So, what can this tell us? Simple, it's not to far fetched to think that the Zora evolved into the Rito. What we know about the placement of TWW and OoT, is that TWW takes place hundreds of years after OoT.

So, this brings me to two theories. First, I'm guessing that Valoo and/or Jabun/Jabu Jabu were told about the mass flooding in advance by the goddesses, and were told to advance the race so that they maybe could not go see old Hyrule. Or secondly, they (Zora) would not be able to survive in a world of large monsters. Water levels rise, and you don't exactly know what is under the waters. PH gives us a good example of that, with the flying whale in all. Evolution doesn't happen unless the species needs to to survive.

Also in a study (from last year) they have proven that evolution can happen in a mere few generations. So, perhaps the evolution of Zora to Rito isn't so far fetched, but the circumstances have to be dire. And if the goddesses deemed it, it could be dire to them.