Although many popular country/western singers recorded a version of the Hank Williams song, which he recorded in the early 1950's the phrase actually goes much further back, historically, and has an entirely different genesis than Willaims' simple lyrics.
Seems that In the early 1800's there were 19 tribal groups of American Indians that joined together and formed the Creek Confederacy, which fought wars with the white settlers who wanted their lands.
They occupied what is now known as Alabama and Georgia. Therefore if the "Lord is willing and the Creek don't rise" up and start up another uprising or battle, we will be able complete what ever it is we intend to do. The approximately 20,000 Creek Indians that still exist reside in Oklahoma.
The proper phrase is "Lord willing and the Creek don't rise". In other words, the word creek actually refers to Creek Indians rising instead of water. (Source: Phrases, Clich�s, Expressions & Sayings)