The film received overwhelmingly positive reviews and won the Academy Award for Best Animated Feature. It was a financial blockbuster as it grossed over $864 million worldwide. It was the 2nd highest-grossing film of 2003, just behind Lord of the Rings: The Return of the King. It is the best-selling DVD of all time, with over 40 million copies sold as of 2006 and is the highest-grossing G-rated movie of all time. In 2008, the American Film Institute named it the 10th greatest animated film ever made during their 10 Top 10. It was also the first Pixar film to be released in May.

After his mate Coral and the rest of their offspring are eaten by a barracuda, Marlin, an apprehensive clownfish who lives on the Great Barrier Reef, is very controlling of his only child. His son, Nemo, has an abnormally small right fin, his "lucky fin", which causes Marlin to worry over his swimming ability. On his first day of school, Nemo boldly ventures away from the reef and touches the bottom of a boat. This makes Marlin angry, and starts an argument in front of Nemo's classmates. To his father's horror, Nemo is captured by a scuba diver and driven away in the boat.

In search of help, Marlin meets Dory, a naïve but optimistic regal tang fish with short-term memory loss. While meeting would-be vegetarian sharks Bruce, Anchor and Chum, Marlin discovers a diver's mask that was dropped from the boat. During a hazardous struggle with an anglerfish in the deep sea, Dory is able to read an address written on the mask as a place in Sydney, Australia. After receiving directions from a large school of fish, Marlin and Dory set out to find Sydney. They encounter dangerous jellyfish and later befriend a surf cultured turtle named Crush while "riding" the East Australian Current (EAC). In the current, Marlin reluctantly shares the details of his journey with a group of young turtles, and eventually, his story reaches Sydney through word of mouth.

Meanwhile, Nemo's captor, a dentist, drops him into a fish tank in his office on Sydney Harbour, and Nemo meets its residents, a group of fish called the "Tank Gang". The gang is led by a crafty and ambitious moorish idol fish named Gill. The fish are frightened to learn that the dentist plans to give Nemo to his niece, Darla, who has previously killed a pet fish in a bag of water by shaking it. Gill gives Nemo a role in his most recent escape plan, which involves jamming the tank's filter and forcing the dentist to remove the fish from the tank while he cleans it manually. Nemo attempts to jam the filter using a rock, and his first attempt fails and nearly kills him, but he later succeeds after Nigel the pelican visits with news of Marlin's journey. The plan, however, is thwarted when the dentist installs a more advanced filter and has no need to take the fish out of the tank.

Upon leaving the EAC, Marlin and Dory become lost in a massive cloud of polluted water and are engulfed in the mouth of a blue whale and carried to Sydney Harbour, where Marlin reluctantly trusts Dory and allows himself to be ejected from the whale's blowhole at the risk of being eaten. They are then met by Nigel, who recognizes Marlin after hearing stories of him and transports him and Dory to the dentist's office. At this time, the dentist has put Nemo into a bag and is preparing to give him to Darla. Nemo plays dead in hope of saving himself, but Marlin sees him and mistakes this act for the actual death of his son. After a chaotic struggle, Gill helps Nemo escape into a drain.

Despite the fact that Dory claims to have better memory when around him, Marlin leaves for home. Dory becomes confused but encounters Nemo, although temporarily confused due to her memory loss, she eventually remembers Marlin's goal, and helps Nemo back to his father. Marlin is relieved to see that his son is alright, but moments later, Dory is caught along with a school of grouper in a fishing net. Making his father realize that he must trust him, Nemo swims to help the fish, including Dory, escape using a trick taught to him by Gill and the other aquarium fish. The three return back home with Marlin less protective of Nemo now that he is aware of his son's abilities. Nemo hugs his father, saying that he loves him and Marlin says that he loves him too. Nemo and his class, including Squirt, a young sea turtle that Marlin and Dory met on their journey, head off to school. An epilogue is shown that the aquarium's filter is broken; the tank gang's escape plan works. They are cheering in the ocean when they suddenly realize they are still in their bags. Their escape plan apparently only went so far as to how to get out of the office.

There are many creatures who do not speak, other fish, the Barracuda, the Anglerfish, the Jellyfish, the Blue Whale and more.

In an interview with National Geographic magazine, Andrew Stanton stated that the idea for the character of Nemo came from a photograph of two clownfish peeking out of an anemone:

"It was so arresting. I had no idea what kind of fish they were, but I couldn't take my eyes off them. And as an entertainer, the fact that they were called clownfish—it was perfect. There's almost nothing more appealing than these little fish that want to play peekaboo with you."

Pre-production of the film took place in early 1997. Film production began, according to IMDb, in January 2000 with a crew of 180. It was Pixar's final use of Sun Microsystems.