It is very likely the database indexes taking up the space, as you noticed it earlier. MySQL (or MariaDB) manages it, and if you have a decently big database, it can take up a lot of space. It is very likely the database cache, it can grew to a huge size with big databases.
Check if you have a database backup running on your server (via SSH), either as a crob job or a process (AutoMySQL or SQLbak). These are automated backups on most linux servers running daily. If it keeps backups of the whole database, then it could very well explain the growth of the size.
Usually these backups keep either 7 or 30 days of backup. If the index and the cache size is around 7-800MB, then a 7 day daily backup will grow the server disk space to around 5G.