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
And here is another which indicates the “Creek don’t rise” originated in the war of 1812.
http://historyiselementary.blogspot.com/2009/10/if-creeks-dont-rise.html
So use Creek for the Indians and crick for the water - works for me.LOL.