A little fish girl lives in an aquarium inside her father's four-flippered submarine. Ponyo is by far the largest of her siblings and is driven by a desire to see more of the world. She has a close call with a dredger and ends up trapped inside a glass bottle and stranded near the shore where she is rescued by Sōsuke, a five-year-old boy whose family lives on a cliff. Sōsuke believes that she is dead until she licks the blood from a small cut he got from breaking the glass from around her.
After taking a great liking to her, Sōsuke names Ponyo and vows to protect her forever.