What I like about the idea is that it contains within itself a great narrative cycle. As a player I could expect my character to go up the river, find adventure, go back down the river. Then go further up the river, find adventure, go back down the river. I like too how the trip back down the river will be faster - after delving a dungeon you want to get home fast!
One fun thing you could have is ways to upgrade the group's boat. They could start with a raft, then over time invest in larger boats, a crew, some weapons, magic sails, etc.