It's not a reliable way to backup. Since files will be being changed, the backup may not be in a consistent state. It shouldn't actually affect the running system (as long as you don't try and backup your backup in an infinite recursion!), but problems could come if you need to do a full restore.
If you need to backup a running system, you need a means to take a "snapshot" of said system. LVM can do this, as can some filesystems, and virtual machines. But these are things you need to set up at install, and I'm guessing you haven't.