Gubble is composed of 10 cities (functioning as worlds); across these are various levels known as "Zymbots", which are usually maze-like in appearance. They are each filled with several enemies and tools. In the PC version of the game, each zymbot is named the same as that of the city plus an additional letter added to the end. For example, the game's first zymbot, which is in a city named "Rennigar", is called Rennigara, while the seventh is called Rennigarp. These zymbots may include bonus levels within them, such as "bonus zymbots", which function as minigames or "special zymbots", which are generally more difficult.

Tools are made to resemble those of a carpenter. A hammer, drill, screwdriver, socket, saw, and a sledgehammer are just a few of the tools used to deconstruct a level. Tools can be found within a zymbot and are used to remove the several nails, screws, hex nuts, etc., which hold a level together. Some tools have other uses, such as moving crates or breaking rocks which serve as obstructions in a level.