The city prison is where most of the show's villains are held, although the one who seems to spend the most time here is Amazing Rope Guy.
It is run by Warden Chalmers and its employees are several security guards, some of which also double as members of the city's police force. The villains are constantly finding some means of escape, whether it’s fooling the guards or digging their way out. The jail is shown to also have a courtyard and other open areas where the villains can walk around, exercise, and socialize, but these areas are surrounded by an electric fence so that they don't try to escape, although the Energy Monster managed to escape in "That's Entertainment" by eating electricity from it to step over it. The villans also sometimes seen doing some sort of manual labor, such as breaking rocks or making license plates. As is mentioned by Dr. Two-Brains in "Dr. Three-Brains", there is even a "Prison Arts-and-Crafts Room", which is where he made his blackout ray, which was stolen by Glen in the same episode.
As is implied by WordGirl in "Oh, Holiday Cheese", there are several other jails in the city, but they have yet to be seen in the series.
At the end of "Lunch Lady Chuck", Chuck was sentenced to serve lunches to the other prisoners in jail, giving Two-Brains a grilled cheese sandwich, Lady Redundant Woman several ham-and-cheese sandwiches, and the Energy Monster a toaster sandwich. There are also places where the villains' friends and relatives can visit them behind glass, as is seen in "Chuck with a Sidekick of Brent", where Brent gave Chuck a sandwich containing the key to his cell.
In The Rise of Miss Power, we see that there is also a large, circular section containing many small cells, where Mrs. Botsford, Reginald, and all of the villains were held, and which they all teamed up to break out of. Many of the townspeople were also kept in the cells where the villains were usually kept. Mr. Botsford and T.J. visited the jail to try to trade prison break material to get Mrs. Botsford out of jail, but their attempt was unsuccessful.
Even WordGirl herself, despite being the show's hero, has gone to jail at least once. In "The Wrong Side of the Law", The Birthday Girl framed WordGirl for stealing the priceless Pretty Princess figurines from Ye Olde Fancy Schmancy Jewelry Store, and Police Commissioner Watson arrested the heroine, who was later proved innocent at her trial and allowed to go back to crime-fighting.
There have also been times when, during mass-heists, all to most of the villains have gone to jail at the same time, usually all in the same cell. Examples would be (in order): "The Wrong Side of the Law", "When Chuck's Mom is Away...", "Where Have All the Villains Gone?", and "Gift Pony".
The Butcher (various episodes)
Kid Potato ("Meat My Dad", "Meat-Life Crisis")
Captain Tangent ("Captain Tangent")
Dr. Two-Brains (various episodes)
Granny May (various episodes)
Chuck the Evil Sandwich-Making Guy (various episodes)
Energy Monster (various episodes)
Hal Hardbargain ("Hal the Haggler")
The Whammer (various episodes)
Lady Redundant Woman (various episodes)
Ms. Question (various episodes)
Theodore "Tobey" McCallister III ("The Rise of Miss Power")
Steve McClean (various episodes)
The Learnerer ("The Learnerer")
The Coach (various episodes)
Timmy Tim-Bo ("Villain School")
Glen Furlblam ("Crime Takes a Holiday", "Dr. Three-Brains", and "Two-Brains Quartet")
Seymour Orlando Smooth ("Win a Shiny New Car" and "Seymour... Right After This")
Amazing Rope Guy (various episodes)