Francis Capra, the young actor who played Elvis (Jesse's half-brother) in Free Willy 2: The Adventure Home (1995) was approached to reprise his role in this film. He declined because he felt that the character of Max was too similar to Elvis.
The end credits featured a memorial dedication to Free Willy co-writer Keith A. Walker who passed after filming for Free Willy 3 was completed.
This is the only Free Willy film not to take place in Oregon in addition to being the only entry to take place in British Columbia, Canada.
The Nintendo game that Max plays when he comes back home from the store at the beginning of the movie, is Star Fox (1993) on Super Nintendo. However at the time this film was released, it's successor the Nintendo 64 was already released a year prior.