As a relentless storm approaches a southern Louisiana bayou community called the "Bathtub" (a community cut off from the rest of the world by a levee), five-year-old Hushpuppy and her unhealthy, hot-tempered father, Wink, are optimistic about their life and their future. The children in school are being taught by Miss Bathsheba about nature and the release of prehistoric creatures called "Aurochs" from the melting ice caps. At home, Hushpuppy fends for herself while her father is missing. When he returns, they argue and Hushpuppy sets her house on fire. A chase ensues between the two, and she ends up getting slapped by Wink. When she retaliates by punching him in the heart, Wink suffers a cardiac arrest. Hushpuppy, having realised the damage she has caused, runs to fetch help only to find her father missing when she returns.
Meanwhile, in the Arctic, the frozen Aurochs in an ice shelf start drifting into the ocean.
Many of the Bathtub residents start fleeing due to the threat of the oncoming storm. Wink reappears staggering along the side of the road and finds and drags Hushpuppy home to start barricading before the storm hits the town. In an effort to make his daughter feel better Wink attempts to scare off the storm by firing a shotgun at the clouds. The next day, the two tour the devastation and connect with the surviving residents. The Bathtub residents celebrate and make plans to rebuild their community, but everything begins to die because of the salt water brought in by the storm surge. Wink hatches a plan to drain the water away by destroying the levee. A little dynamite does the trick, the water recedes but it doesn't matter, and it brings the authorities who force the mandatory evacuation order, removing the inhabitants of the Bathtub to an emergency shelter. There, Dr. Maloney performs surgery on Wink, but it doesn't restore Wink's health. At the first opportunity, the evacuees storm out and escape back to their homes.
Aware of her father’s condition, Hushpuppy leaves in search of her mother. She and her friends swim to a boat which takes them to a floating bar. Hushpuppy meets a waitress who may be her mother, though the woman doesn't recognize her. She wants to stay but the waitress tells her she can't take care of her. Hushpuppy and her friends return home, where she confronts the Aurochs freed from the ice caps and recognizes the animals as friends. As the Aurochs leave, Hushpuppy enters her home and says her last goodbyes to the dying Wink, listening to his last heartbeat. She sets his funeral pyre ablaze, standing in solidarity along with the remaining residents of the Bathtub.

Quvenzhané Wallis as Hushpuppy
Dwight Henry as Wink
Levy Easterly as Jean Battiste
Gina Montana as Miss Bathsheba
Lowell Landes as Walrus
Jonshel Alexander as Joy Strong
Marilyn Barbarin as Cabaret singer
Kaliana Brower as T-Lou
Nicholas Clark as Sticks
Henry D. Coleman as Peter T
Philip Lawrence as Dr. Maloney