All the episodes generally follow the same format:
The episode starts with a sketch of Molly saying "Hi, it's me, Molly, and it's time for-" only to be stopped by Gil performing an act related to the episode's subject; such as using a jackhammer in Build Me A Building!, or sleeping in a tent in The Legend of Pinkfoot!. One of the two then states "It's time for Bubble Guppies!", and the theme song plays. After the theme song, the Little Fish say the episode's name.
Something occurs when a character or two who goes to school (example: Avi breaks his tail in Call a Clambulance! when Oona was going to school) the character or characters plays a major role in that plot. After that, the school day begins and the Bubble Guppies say "Good morning, Mr. Grouper!". Later, the remaining Guppie tells Mr. Grouper about what happened earlier. He states "Let's think about it," and the characters discuss the topic. The pop song focusing on the episode's main topic then begins.
One of the Guppies will go to a shop that mostly focuses on the topic (example: a doctor's office in Call a Clambulance!). The owner of the shop will asks questions about what he or she needs. Later, Mr. Grouper comes into the shop and says it's time for lunch, and the "Lunchtime" song plays. At lunch, three of the characters make a food joke about the subject of the episode (example: Molly gets pizza and a banana, Oona gets a sandwich and a cookie, and Deema gets a sandwich and an ice cream "sun"-dae in The Moon Rocks!''). After lunch, another Gil and Molly sketch is shown.
The Guppies do something fun which can determine another important character and leads Mr. Grouper talking more about the topic, which leads into a dancing song; though the order of the songs varies from episode to episode. Mr. Grouper then says it's time to go outside, the "Outside" song plays, and the Guppies act out a story about the topic, interfered with Adobe Flash-animated graphics. After this, Gil and Molly do another sketch.
The Guppies go on a field trip that focuses on the topic where it sometimes focuses on a problem shown in the beginning and involves the important characters and might determine another one, and the show concludes with the last Gil and Molly sketch and a reprise of the theme song.
