MacOS Sequoia filling up with system data

I'm also drowning in (428GB of) System Data. It seems it doesn't even matter if I'm removing other files from my laptop, I'm not getting any space back.

What seems even weirder is that I can't seem to find where these 400GB are hiding...

Spotlight or more precisely mds_stores is writing huge amounts but they are disappearing instantly and NOT filling up my drive.

However it is still creating immense wear which will eventually destroy my SSD.

The only "cure" I have found is to drag all my drives into the "do not search" box of Spotlight in System Settings.

This has reduced the total writes from over 100 GB per day to a normal 12 GB daily but of course it means Spotlight won't work.

I've never found it to be much good so I am not too bothered by its loss but it would be nice to have a fully functional machine even though I don't need it.

First of all, thank you SO much for the extremely quick response!

I'd say about 10 minutes after I posted my previous message - and while I was using Disk Inventory X to scan for any hidden huge folders - my Mac suddenly decided it felt 200gb lighter..

I'm not sure if the actual folder scanning did anything or it just randomly felt like unclogging the drain, but I'm not sitting comfortably at 'only' 200gb system data...

Hi,

Your Mac “System data” contains files that don’t fall into the categories listed here (Apps, Document folders, iCloud Drive, iOS Files, TV, Music, Books, and Podcasts Mail, Messages, Music creation, photos, trash, apps and files from macOS). 

This category primarily includes files and data used by the system, such as log files, caches, VM files, and other runtime system resources. Also included are temporary files, fonts, app support files, and plug-ins. You can't manage the contents of this category. The contents are managed by macOS, and the category varies in size depending on the current state of your Mac.

You will have to navigate through your files in library to clear this " system data". I have created a video about this with steps.

You can have a look and see if you are able to follow it : https://youtu.be/9P4oqri4dYc?si=1WT4JKtmYfdnfTrd

Exact same story here with Mac M1 Pro - Sequoia update exploded the system data and deleting items from documents seems to only shift data from there to system. I trashed 260GB of video from documents and saw a corresponding increase in system data. I don't use time machine. Other fixes suggested don't do anything. Lack of free space seems to be causing other buggy issues with performance and random rebooting. Would love an actual update to fix this, or easier way to downgrade to macOS 14.

Since macOS Sequoia, there is a way to link files and folders similar to a hard link that is only available for macOS. This is called a "firm link". Such "firm links" cannot be created by the user. These "firm links" are used to link the user-writable folders on the boot disk to /System/Volumes/Data. Apparently, the built-in terminal tools such as 'du' or 'df' as well as the third-party desktop app 'DaisyDisk' cannot yet handle these new "firm links" correctly in every case and the disk space for the linked areas may be counted twice. This mainly affects the content of /Users, /Applications and /opt

I also have a lot of System Data after upgrading to Sequoia. It's only 60 GB, but that's 1/4 of my 256 storage capacity. Is this a glitch in the system? Is any of this data non-essential and purgeable?

I have the same issue since upgrading to Sequoia: lots of space before, full disk after.

As @DGaryC said, this has nothing to do with normal files in Documents, Downloads, Photos, etc. It's a sudden bloating of System Data after upgrading to Sequoia.

A few days ago I noticed that the disc usage had jumped from approx. 50% to 90% (Mac M1 Sequoia, 512 GB SSD). The system data suddenly occupies more than 200GB. When analysing under root, I found that all non-linked root folders (/Applications, /Users etc.) are also present in the /System/Volumes/Data folder with the same inode numbers. Linked or mirrored - no idea. If mirrored, this would mean that since Sequoia only about 50% of the disc is effectively available... If linked, all the disk (usage) utilities should be updated a.s.a.p...

Until now, common tools for disc usage (e.g. DaisyDisk, df, du) calculate everything there twice. 

Scanned with du in "/System/Volumes/Data":

iMac:/System/Volumes/Data$ du -m -d 1 -x 2>/dev/null

...

11498 ./Library

2295 ./System

3339 ./private

196761 ./Users

20745 ./Applications

33626 ./opt

...

Total: 272983 .

Scanned with du in "/":

iMac:/$ du -m -d 1 -x 2>/dev/null

...

11498 ./Library

284634 ./System (with ./Volumes/Data/...)

3340 ./private

196766 ./Users

20745 ./Applications

33626 ./opt

...

Total: 551301 .

Nothing is what it seems at first - With the standalone version of DaisyDisk I got a deeper insight into the structure of the system data on the disk. It turned out that the remote backup software I use, 'ChronoSync', necessarily creates or uses an APFS snapshot volume. The size of this third party snapshot corresponds to the size of the data to be synchronized and is approx. 120 GB in my case. The rest of the system data is occupied by macOS. E.g. by TimeMachine snapshots and other areas that are not accessible to the user. The output of the command line program 'du' was particularly confusing for me.