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My D: drive of 137GB (NTFS) would appear to be full, but I personally disagree. This are the reasons I disagree with reality:

  1. Selecting all files and viewing their properties, it says 43.4GB size and 43.8GB size on disk. Because the size on disk is nearly identical, I don't think I have a million tiny files filling up sectors.
  2. In Explorer I show hidden files and also protected system files, so explorer includes as much data as possible when counting the above size and size on disk.
  3. Viewing the partitions' contents using 'SYSTEM' permissions (which are above 'Administrator'), there are no huge files in System Volume Information and no other invisible directories.
  4. SMART has always been enabled and is currently not showing anything weird.
  5. The partition/disk does not have anything in the read/write cache. I've used sync and, after that didn't work, also tried rebooting. I didn't do a cold boot (that sometimes tends to help even if rebooting doesn't fix something. Should I try that?).

The reasons that make me think the disk is full at all is that Windows cannot create new files (from explorer nor any scripting/programming language), and because when viewing the partition's properties it reports to have used all 137GB.

What might I have missed? Where did all my free space go? How can I view what's taking up all the storage space and get rid of it?

When cleaning stuff up, space is indeed freed again and I can reoccupy it with other data. I've also recently cleaned up a directory with ~160 000 small (80 byte) files, which did clear up a couple of megabytes (though I'd expect it to clear up 160000*4KB (sector size) instead of the 160000*80B which it did), but I still can't find anything that might occupy two thirds of the entire partition.

Unfortunately I'm talking about a server and I don't have the luxury of owning redundant hardware, so I'd prefer not to have to boot from a live stick if in any way possible. I guess I could do some scheduled nightly maintenance if there is really no other way to inspect or repair things properly, but I'd like to keep that to a minimum. I am somewhat experienced with GNU/Linux so I'd know my way around on a live boot command line if you tell me which commands/tools I should check out.

Edit: By the way, NTFS compression is not enabled.

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Run TreeSizeFree as admin and look which folders use most space. – magicandre1981 Jan 28 '14 at 4:58
Run spacemonger as admin and see. Spacemonger v1.4 is still available for free. 2 Biggest offender is usually pagefile.sys (not much you can do here, it will be as big as much RAM you have), and hiberfil.sys (as Suriyan mentioned). You can delete hiberfil.sys by turning off Hibernate feature by typing powercfg -h off on the Command prompt (as admin). – Darius Jan 28 '14 at 5:43
another space saving technique , one I did in XP, is (assuming system restore is on) to turn system restore off then on.That wipes the system restore directory which can be pretty big, that was in XP anyway. but I second the above mentioned of treesizefree by jam and just tried spacemonger 1.4(which is free), looks good. – barlop Jan 28 '14 at 6:09
What's your operating system? First thing you can try is to run the Disk Cleanup tool as administrator and see how much space is taken by temporary files and the like. – and31415 Jan 28 '14 at 11:00
NTFS doesn't work as you think. If the file contents (a $DATA attribute) are small enough, they are stored entirely within the MFT entry. An 80 byte file, presuming that all of its other attributes can be resident as well, might not occupy any disc blocks other than its MFT entry. – JdeBP Jan 28 '14 at 12:29

I've found the issue. Turns out there was a folder that could only be accessed with SYSTEM permissions somewhere deep down a directory tree. The way I checked for files with SYSTEM level permissions is through FileZila Server: it automatically runs as system service and with an ftp client you can view all files (even in System Volume Information). But because the directory name starts with a space and Filezilla bugs on that, the directory appeared to be empty from Filezilla's point of view.

All in all, a combination of circumstances that made me miss a huge directory somewhere. Nothing fishy in NTFS or Windows going on after all.

The way I found it eventually was by running spacemonger as suggested by @magicandre1981 in a comment. I didn't expect to find anything more than what other programs already had (I already used some space indexing tools), but this one also told me which directories it couldn't scan (namely System Volume Information, and the one I had overlooked). I then changed ownership of the directory so that I could enter it as administrator, and removed all the files.

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How much memory do you have installed? This will certainly influence the size of pagefile.sys and hiberfil.sys, which on my machine occupy 20GB and 15GB respectively.

Here's an explanatory article

WinDirStat will show you visually the space occupied by your files.

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I know what the pagefile and hibernation file are, and I would have seen them if they were there (I mentioned I've set explorer to show hidden and protected files, and even checked with system level permissions). They're located on the C: drive. Also I've run a program similar to WinDirStat and all it can find is 43GB of data, no more. All the rest is empty space, according to that program. – Luc Jan 28 '14 at 13:56
as others already said use spacemonger or maybe rather spacesniffer (I like that one) and you will see graphical diagram of all the drive's content. Maybe there will be something visible. It would be also interesting if you posted a screenshot of it's result here. Also please right click "computer" / manage / disk management and post a picture of that too. – Vitas Jan 28 '14 at 14:08

In the case that you mention if that was a laptop and you are putting the laptop in hibernate and using it for many days, a huge area is occupied by temporary files. You can recover the disk space by removing those temporary files from the system. The cleanup wizard won't necessarily delete all temporary files.

You can open the temporary files folder from Explorer by just pressing Win+R and entering %TEMP%.

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%TEMP% is located on the C: drive, and I would have seen it if it was occupying space on the D: drive. The hibernation file is also on C:, and again, I would have seen that. – Luc Jan 28 '14 at 14:00

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