Ok so the note says "the underground river is hidden well." So I'm thinking it has something to do with a well, but the only well I know about I can't seem to do much with. Am I going about this hint the right way or am I way off?

Well, that is one of the vaguest hints in the game, so what I'll say is that you are on the right track, take a look at the level, and see if there is anything that stands out.

Found the hidden piece, it was so small I missed it the first few times. Thanks Jon!

No problem, glad I helped. :)