The show has established a few running gags that pop up in several episodes.
- Chris Bradford and Xever defeated by water -In earlier episodes, these villains always seemed to be defeated by a rush of water as seen in New Friend, Old Enemy, Never Say Xever, and The Gauntlet, but in The Gauntlet, Chris Bradford & Xever were flushed down by Mutagen.
- Michelangelo, Naming Master - Michelangelo has given names to nearly all of the villains and gadgets on the show and was visibly angered when the Rat King named himself.
- The Turtles always mispronounce Baxter Stockman's name - At least once in every episode Stockman appears in, his name is butchered, either by the turtles or other characters. Favorite mispronunciations include: Dexter Speckman and Boxer Stockboy.
- Leatherhead grabs Donatello by the face - In both of the first episodes where Leatherhead has appeared, It Came From The Depths and TCRI, he has angrily grabbed hold of Donnie's head during one of his rages.
- Kung fu frogs - Every time the turtles encounter Spider Bytez, he always thinks they are frogs and that they use instead of Ninjutsu. Hence, he calls them "Kung fu frogs".
- Space Heroes/Super Robo Mecha Force Five/Crognard the Barbarian - In almost every episode, the gang watches a show that turns out to have the exact same situation they get into.
- In Season 3, each time the Turtles defeat a mutant, mutagen gets spilled and inadvertently creates a new mutant.
- Splinter often teaches a lesson to the Turtles that comes in handy on missions.