The show features the adventures of three major characters: Lazlo, the title character, is a Brazilian spider monkey with a carefree attitude; Raj, an Indian elephant who is more level-headed; and Clam, an albino pygmy rhino, who speaks in bursts of one or two words, synonymously echoing his friends statements.

Each episode is split into two parts approximately 11 minutes long, with the exception of two episodes. The show breaks the fourth wall, such as when Lazlo gives an award to a camper for being the best "incidental character",and sometimes lacks continuity, as in an episode which ends with Lumpus being eaten by a lake monster.

The story revolves around Adam Lyon, a human student at Charles Darwin Middle School. After a clerical error listed his name as "Lion", he is sent from Chester A. Arthur Middle School to Charles Darwin Middle School, a school for the local zoo animals. Shortly after his transfer, he is partnered with Jake Spidermonkey in gym, hence the title. While Adam has to deal with the obvious difficulties humans have performing animal-like tasks, Jake just has fun at everyone else's expense. Jake also seems to be quite attached to Adam, going into deep depression when Adam hangs out with other friends or is away for awhile. This is exemplified by Jake publicly crying when Adam is sick for a day.

Much of Charles Darwin Middle School is modeled after specific habitats. For example, there are fish tubes created so that the fish can breathe and swim around. There are also vines and bodies of water. Though some animals like Bull Sharkowski use devices to allow them to live outside of their natural habitat. In Bull's case he uses what looks like headphones full of water that go around his gills. The main characters have been able to breathe in water in the pilot episodes for some strange reason.

Charles Darwin Middle School appears to be the only animal school around, as it is later explained in the episode "Uniformity." In the episode, there are high end east coast schools for animals. The school competes against human schools in athletics and other events. In one episode where Adam signs up to return to his old school for a day transfer, all the teachers and staff seem to replicate their animal counterparts.

The Powerpuff Girls revolves around the adventures of Blossom, Bubbles and Buttercup, three little girls with super powers. The plot of a typical episode is some humorous variation of standard superhero and/or tokusatsu fare, with the girls using their powers to defend their town from various villains, such as bank robbers, mad scientists, aliens or giant monsters, and often dealing with normal issues young children face, such as bed wetting or dependence on a security blanket. The show is one in a long line of cartoons that derives a great deal of humor from pop culture parody and satire.