I know this is a cover of a (Howard Seratt i think?) song, but have been listening to it a lot lately.
My interpretation of the song, it seems the 'Troublesome Waters' are a metaphor for someone battling their own demons....
"out on the ocean i've seen mans despair"
an being guided by God or whatever
"gently i feel the touch of his hand guiding my boat to that better land"
Don't know if it's a christian song or what but it gives you a good kick up the arse when you feel a bit down. Just shows how cryptic lyrics can be sometimes and it pays to listen a few times.
Anyway..... good cover.