Das Arch-Wiki sagt dies dazu (ich habe es aber noch nicht ausprobiert):
Encryption
Btrfs has no built-in encryption support, but this may come in the future. Users can encrypt the partition before running mkfs.btrfs. See dm-crypt/Encrypting an entire system.
Existing Btrfs file systems can use something like EncFS or TrueCrypt, though perhaps without some of Btrfs features.