During two months of filming in Alabama, the production endured muggy heat, swarming bugs, a mysterious "killer" mulch that made several people sick, severe thunderstorm warnings, and a tornado watch.
Originally Elijah Wood was going to reprise his role as Huckleberry Finn to make this film set in the same world as The Adventures of Huck Finn (1993) (also written by Sommers), but was too busy filming Flipper (1996). He was replaced by Brad Renfro.
Twelve-year-old Brad Renfro had a much older girlfriend during filming.
This is Rachael Leigh Cook's film debut.
According to Mark Twain the source novel is largely autobiographical. Tom Sawyer is based on Twain. Huck was based on Tom Blankenship, a boy Twain befriended in Hannibal, MO. He was the son of a local vagrant, who Twain said "had the greatest heart of anyone he knew". Becky was based on Laura Hawkins, who Twain dated for a while. Injun Joe was based on Joe Douglas, a local vagrant who spent half his time in jail. He was very sweet to the local kids when drunk, but could be scary when he sobered up.