The pair, who recently filed for divorce, made the decision to temporarily leave the West Coast amid their divorce announcement, reported Us Weekly Magazine.
"They got the kids out of LA as soon as school was out. Bahamas is a place they've been going to for years that's very private and special for their kids.
"When either of them have had work commitments they have been leaving to go fulfil them," a source said.
Affleck and Garner will continue to live on the same property in LA's posh, celeb-friendly Brentwood area, but will live in separate residences, according to the source.
"They are going to try and model their divorce like Gwyneth and Chris. They feel like they have to be mature adults for their children's sake and that they will figure out the healthiest way to co-parent.
"They want the kids lives to stay the same and to not have to change just because they aren't going to be married anymore," the insider said.