"We're going the wrong way. The river is over there." Maybe it curved in around itself? The Zora River was so curvy that it touched on almost all the regions of Hyrule. On the other hand, it wasn't deep enough to have boats on it, much less ships.
"Hey, those are trees. What is this, like a--whoa!" Epona had come trotting up on her own, apparently sensing Link in the area. "Hey, girl, how'd you get so big?" Link ran up to her and patted her on the neck. She gave Link a few sniffs, decided that it was just one of those Hero of Time things, and licked his face. "Come on, Edward's taking me to her ship. I didn't know you liked the water."