System Data over 500GB unable to identify problem

I have an M2 Mac Mini with 1TB hard drive. Lately I have been struggling with free space below 100MB. I looked and found to my horror that System data was over 500GB. I tried all the usual remedies, deleting caches and old time machine snapshots, to no avail.


I spent hours trying to find out and diagnose the problem. In the end I decided that the only thing I could do was reinstall and restore. As this is a length process, I decided to first try using SuperDuper, to clone my startup drive and restore it. IT WORKED! Now my System data is 3GB and I have 700GB free space.


I'm not posting this to find a solution, I found one, I'm posting it, because I see many others have experienced the same problem.


[Edited by Moderator]

Mac mini, macOS 26.1

Posted on Nov 7, 2025 8:08 PM

Reply
10 replies

Nov 9, 2025 9:07 PM in response to Guyus

Guyus wrote:

Of course not, but I’m suspicious of some sort of memory leak, or failure to manage temporary files (not visible to the user). From what I’ve read, some people just experience a large amount of system data which can easily be purged, but I’m seeing more reports like mine where the system data is half the hard disk and growing. The usual fixes don’t do much. It’s frustrating due to the nature of APFS. I’ve never experienced such issues with other file systems like FAT, FAT32,ExFat, HPFS, NTFS etc

What I'm saying is, I think there is an inherent problem with APFS, which causes this massive increase in System Data, which cannot be identified by the user.


Understood.


you can throw HFS+ onto that list...



you can file a bug report / submit your Apple Feedback here:  Product Feedback - Apple


Nov 9, 2025 9:09 PM in response to Guyus

System Data is merely a catch-all for data that Spotlight can’t place in one of the designated categories. Cache files, etc., are common culprits.


This sort of thing is not uncommon with macOS upgrades when people have software/extensions installed that are incompletely compatible with the new version of macOS, recently and years ago when System Data was called ‘Other’ (probably a more accurate label).

Nov 9, 2025 8:40 PM in response to Guyus

Of course not, but I’m suspicious of some sort of memory leak, or failure to manage temporary files (not visible to the user). From what I’ve read, some people just experience a large amount of system data which can easily be purged, but I’m seeing more reports like mine where the system data is half the hard disk and growing. The usual fixes don’t do much. It’s frustrating due to the nature of APFS. I’ve never experienced such issues with other file systems like FAT, FAT32,ExFat, HPFS, NTFS etc


What I'm saying is, I think there is an inherent problem with APFS, which causes this massive increase in System Data, which cannot be identified by the user.

Nov 9, 2025 9:17 AM in response to Guyus

Guyus wrote:

I have an M2 Mac Mini with 1TB hard drive. Lately I have been struggling with free space below 100MB. I looked and found to my horror that System data was over 500GB. I tried all the usual remedies, deleting caches and old time machine snapshots, to no avail.

I spent hours trying to find out and diagnose the problem. In the end I decided that the only thing I could do was reinstall and restore. As this is a length process,

I decided to first try using SuperDuper, to clone my startup drive and restore it. IT WORKED!

Now my System data is 3GB and I have 700GB free space.

I'm not posting this to find a solution, I found one, I'm posting it, because I see many others have experienced the same problem.

[Edited by Moderator]


Good computing Guyus !

Nov 10, 2025 2:31 AM in response to Guyus

Sorry but using a Cloning Software like Shirt Pocket SD or CCC Carbon Copy Cloner to make a Clone


By Definition a Clone would make a replica of the existing 1 TB drive onto an external drive


Reversing the process from the Cloned Drive back to the 1 TB by definition of Clone


Would it not bring everything back


If it did not bring everything back, this could not have been a true clone

System Data over 500GB unable to identify problem

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