Documentary filmmaker Elly Thompson learns that hundreds of people have disappeared on the Mississippi River where she grew up. Years before when Elly was five, her father disappeared while she was out on the river with him. When Elly receives a newspaper clipping about another man's disappearance, she decides to travel back to her hometown to learn the truth about why her father disappeared and why she was spared.

She takes her crew, consisting of her camera man and ex-lover Matt, research assistant Eva and sound technician David. They hire a plain-speaking river man named Jack to take them up river to the site of the disappearances, despite the fact that he thinks their mission is foolish.

The desolate landscape begins to prey upon the fears of the group of five. As the elements grow harsher, and as the group becomes trapped by inexplicable changes in the landscape, one by one the characters begin to break down psychologically. Elly must try to hold her crew together as the secrets of what happened Beneath the Mississippi all those years ago are revealed.

Beneath the Mississippi evokes the paranoia of Alien or Poltergeist, the disturbing psychological journey of Apocalypse Now and the satisfying payoff of such horror films as The Others.