He had less success in 1999 with Kevin Smith's irreverent comedy Dogma, costarring Damon and Chris Rock, and the poorly reviewed romantic comedy, Forces of Nature, costarring Sandra Bullock.

In 2000, he turned in a supporting performance in the slick stock-market drama Boiler Room, and headlined the fast-paced action thriller Reindeer Games, costarring Charlize Theron and Gary Sinise. He also costarred opposite Paltrow in the romantic drama Bounce. In the summer of 2001, Affleck reteamed with Armageddon director-producer team Michael Bay and Jerry Bruckheimer for the extravagantly marketed World War II-era action epic, Pearl Harbor, costarring Kate Beckinsale, Josh Hartnett, and Cuba Gooding Jr., and budgeted at $135 million.

Affleck has a younger brother, Casey, who is also an actor—he appeared with his brother in Good Will Hunting and 200 Cigarettes (1999), and starred opposite Heather Graham in Committed (2000). Affleck and Paltrow announced their breakup in late 1998, but remain good friends.

In August 2001, Affleck checked himself into an exclusive rehabilitation center in Malibu, California, to undergo treatment for alcohol abuse. The son of an alcoholic (his father, Tim, has been sober since 1990), Affleck announced through a spokesman that he has "decided that a fuller life awaits him without alcohol.".