If you want to use baobab, this is possible by mounting the root filesystem in another place and analysing that. This way, other filesystems will not be mounted in the new root mount and any files hidden by mounts under
/ will be uncovered and counted in your analysis.
Assuming your root filesystem is on
df will tell you which device it is):
> mkdir deleteme-later
> sudo mount /dev/sda1 deleteme-later
> baobab deleteme-later
and then tidy up when you're done:
> sudo umount deleteme-later
> rmdir deleteme-later
Alternatively you could unmount said file systems manually. You can also scan just your home folder, because it will most likely contain the source of the excessive disk space usage.
du has two options which are able to prevent counting other filesystems:
skip directories on different file systems
exclude files that match PATTERN
would ignore all other mounted filesystems or
du -h --exclude /media
would ignore all mounted filesystems in /media.
If you're using
du, sorting so that the biggest things appear at the bottom of the list can help decipher the output. eg:
du -hx | sort -h