The films plot is primarily based on seven A. A. Mline stories: "In which Pooh & Piglet go hunting and nearly catch a Woozle" (Chapter III of Winnie-the-Pooh), "In which Piglet does a very grand thing" (Chapter VIII from The House at Pooh Corner), "In which Eeyore finds the Wolery and Owl moves into it" (Chapter IX from The House at Pooh Corner), "In which Tigger comes to the forest and has breakfast" (Chapter II from The House at Pooh Corner), "In which Piglet meets a Heffalump" (Chapter V from Winnie-the-Pooh: Winnie the Pooh's nightmare of Heffalumps and Woozles), "In which Piglet is entirely surounded by water" (Chapter IX of Winnie-the-Pooh), and "In which Christopher Robin gives Pooh a Party and we say goodbye" (Chapter X of Winnie-the-Pooh). In A. A. Milne's original story Pooh shows more initiative during the flood, finding his way to Christopher Robin by riding on one of his floating honey pots, which he names The Floating Bear, then having the inspiration of using Christopher Robin's umbrella to carry them both to Piglet's house.
At the beginning of the story, Gopher tells Winnie the Pooh that it is "Winds-day" (a play on "Wednesday"), where upon Pooh decides to wish everyone "Happy Winds-day". He visits his friend, a young pink pig named Piglet, who wears a scarf around his neck on this day. Piglet is blown into the air, his scarf unravelling all the while, and Pooh grabs hold of him. As they fly like a kite through the air, over the other characters' heads, Pooh wishes Kanga, Roo, Eeyore, Rabbit, and Owl a happy Winds-day. However, once they arrive at Owl’s treehouse, he informs them that the wind is due to "a gentle spring zephyr" rather than to a particular holiday. During the windstorm, Owl's house is knocked down, so Eeyore volunteers to house-hunt for Owl.
That night, Pooh hears an unfamiliar noise coming from elsewhere in the Hundred Acre Wood. Someone knocks on Pooh’s door, then a bouncing, boisterous and exuberant tiger named Tigger bounces inside in search of something to eat. After Tigger sings his signature song, "The Most Wonderful Thing About Tiggers", he tries some honey but decides, "Yuck! Tiggers don't like honey!". Before leaving Pooh’s house, Tigger tells him that there are Heffalumps and Woozles in the forest and that they steal honey, Pooh's favorite food. Later, Pooh suffers from a nightmare in which Heffalumps and Woozles steal his honey while the song "Heffalumps and Woozles" plays.
Later that night, a storm floods the Hundred Acre Wood. Piglet, who is trapped in his home, writes a bottle-note for help, just before the waters carry him away, him riding a chair. Pooh, who is trapped in a honey pot, floats away from his home as well. The remaining beloved characters gather at Christopher Robin's house, and Christopher discovers and reads the message ("Help! P-P-P-Piglet [Me]!"). He then sends Owl to inform Piglet of a rescue plan in the works, but just after he delivers the news, Piglet and Pooh are mixed up in a waterfall which switches Piglet to the honey pot and Pooh to the chair. When they arrive together at Christopher Robin’s house, he mistakenly thinks that Pooh rescued Piglet, and throws a hero party for Pooh.
During the party, Eeyore announces that he has found a new home for Owl. But everybody, unfortunately, learns that the one Eeyore found is Piglet's house. They are shocked and dismayed and try to tell Eeyore that Piglet already lives there. However, Piglet decides to reluctantly give his home to Owl, to which a touched Pooh offers to let Piglet live with him. Pooh suggests to Christopher Robin that the hero party should become a two-hero party because of Piglet’s generosity. He agrees, and the characters celebrate both Pooh’s and Piglet's good deeds that day.