Well, no matter where it came from way back when - I always heard it used to mean water might flood the road - only thing is we always said “crick” not “creek”. LOL
We still have plenty of people in our rural district who can become housebound for a few days when the low water bridge gets covered by water from the “crick”. LOL.
After a non-exhaustive search, it seems the jury is still out on origins of the phrase.
Wickipedia has it as small streams of water flooding, and another site, “ Wicki Answers” has it as the Creek Indians...but that is not final. They both work, and I like the dual imagery!
http://en.wiktionary.org/wiki/Lord_willing_and_the_creek_don’t_rise
http://wiki.answers.com/Q/Where_did_The_Lord_willing_and_the_creeks_don’t_rise_come_from