I'm starting to not be so sure that Koholint is/was as objective a reality as I thought it was. The game itself calls Koholint an illusion. The Nightmares say that they were "born of nightmares." 

Can we agree on a scenario like this? Link is shipwrecked, and hangs onto some flotsam before passing out. In his dark dreams he has nightmares of Ganon returning and conquering the world. Meanwhile, the Wind Fish (location undisclosed) is dreaming of Koholint. Suddenly, Link and the Wind Fish share the same dream. The Wind Fish's illusion seems so real that Link thinks he has actually washed up on a real shore. In fact, Koholint and the Nightmares don't exist in objective reality; Link's nightmares are combining with the Wind Fish's dreams, and the Wind Fish has such vivid dreams that, to Link, they seem like reality. At the end, Link and the Wind Fish awake together. Link wakes up to find himself where he's been all along: hanging onto a piece of flotsam. The Wind Fish wakes, but has enough creative power to recreate Marin in objective reality. 

If the above scenario is true, then centuries couldn't have passed while Link was dreaming. In objective reality, Link was hanging onto a piece of flotsam while he was sharing in the Wind Fish's dream. He couldn't have been floating in the water for centuries, or when he woke up he would find that the flotsam had rotted away centuries ago and he was a drowned skeleton.