Sometimes in a story the setting is a character. That is, the setting plays such an important part in the story, and seems to take on a role of its own. In this case, the events could not have happened in any other setting, so the nature motif helps to bring the power to the setting.
The river is personified repeatedly in The Wild Palms and obviously plays a big part in half of the narrative, where the prisoner fights against the river to save the woman then return to custody.
Looking at any of those sections, you should find ample examples of nature represented as chaotic and as standing against human reason/human intentions.
In a way, this is a book about the mysteries that underly human behavior and nature functions as a metaphor for those deeper motivations (which drive the prisoner to seek captivity and run from freedom and which drive the man and woman to desperately love and hate one another, shunning success and society in favor of love in isolation).
The reverse flow of the Mississippi is a parallel to the seemingly unnatural actions of the characters.