It might be a good idea to decrease Magento size on disk and number of files before doing a backup.  This way your backups will be smaller and faster and the restore will take less time.

Using a command: ( from Magento 2 root directory )

du -a . | sort -n -r | head -n 20

Will show you which files / directories take up most of your space

In our case it was 

/pub

/var

So repeating the command 

du -a var | sort -n -r | head -n 20

Will show what directories take space inside the var directory.

In our case we had a lot of imports and exports and some cache and logs: 

pub/media/catalog/product/cache

var/log/cron.log

You can repeat the above for the /pub directory

du -a pub | sort -n -r | head -n 20

Next thing to do would be to delete some unused images - You can see our post on how to do that:

Delete unused images

It is a good idea to setup cron job to clean up the cron.log inside Magento root/var/log ( We will soon add more information about that )