The story is complicated, and some critics say a bit too complicated, but it's based on a true story, and sticks fairly close to the actual historical events. If anything, what really happened is even more bizarre and twisted that what is in the film. There's only one major discrepancy between historic events and what's portrayed in the film.
Spoiler
In the film, the information about the murders at the chicken ranch becomes known while Angelina Jolie is in the nut hatch and the publicity is the reason she is released. In real life, the murders did not come to light until after the disappearance case had resolved itself and Jolie's character was released from the nut hatch. The reason she was actually released was because the impostor boy finally confessed that he wasn't the missing child but that he had made the story up so he could see California.
It's not quite at the level of Mystic River, but it should certainly stack up as one of the best films of the year.