Michael Keaton was originally cast as Sean Devine. He had done several script readings with the rest of the principal cast, and he had been doing research for the role with the Massachusetts State Police Department, and living in Boston for several weeks. A month before principal photography was to start, Keaton and director Clint Eastwood got into a huge argument, and Keaton left the project. A week later, Kevin Bacon was cast in the role.
The situation at the opening of the movie is based on an incident when, as a child, author Dennis Lehane's mother castigated him for getting into a car with men who claimed to be plainclothes policemen.
The studio executives at Warner Brothers wanted Clint Eastwood to shoot the film in Toronto, Canada to save money. Eastwood refused and pushed to have the film completely shot in Boston where the film is set.
In the beginning of the movie when a young Dave is thrown into the backseat of the car, a man in the front seat turns around and flashes his ring - a bishop's ring. The book never indicates that the character was a priest, but it was added to the film since the filming was right in the middle of the priest scandal in the Boston Archdiocese.
In Sean Penn and Tim Robbins's only previous feature together - Dead Man Walking (1995) - both were respectively Oscar-nominated as Best Actor and Best Director. On this one, both were victorious as actors.
At a press conference for his movie Mystic River (2003), Clint Eastwood condemned the Iraq war as a "big mistake" and defended Sean Penn's visit to Baghdad, saying he might have done the same thing but for his age.
More than 2,000 people who wanted to be extras in the movie showed up at the Boston Teachers Union on 14 September 2002 for the open casting call. Carolyn Pickman of Collinge-Pickman Casting told The Boston Globe a week later that about two-thirds of those trying out would be called to fill a church and a local bar, play spectators at a parade, or walk through other scenes. All types of people from the greater Boston area (and as far away as New Hampshire) attended the call, where they waited in long lines to eventually hand in their applications and get their pictures taken.
The liquor store scene was shot at Costello's, a liquor store on Boylston Street in the Back Bay, next to Berklee College of Music. After filming, screen shots from that scene were placed in the front display windows. Costello's closed in January 2007.
Kevin Bacon and Laurence Fishburne portray State Police partners Devine and Powers in this Mystic River. They first co-starred together as rival bicycle messengers Casey and VooDoo in the 1986 urban thriller Quicksilver, a feature film where Bacon was the headliner.
The tombstone scene was shot in Roslindale at Wellsmere Monumental Works, as it had the background of an overground field on two sides of it and on the other side an old 1820's house that still stands at 3849 Washington Street.
During the scene where Sean Penn's character steps into the morgue where his daughter Katie (Emmy Rossum) is lying on the slate dead, and when he is emotionally promising revenge, Rossum burst into tears, saying that "the scene was so powerful and moving and Sean Penn was so amazing".