OK, I'll do my best to try to clarify what's happening here.
First, what is being represented by that percentage is not in relation to space/capacity on the hard drive, but to input/output (most often abbreviated I/O) activity to same.
It is very common when you open Task Manager for there to be a brief "blip" of very high disc activity and, in your screen shot I am presuming that's what you're seeing since "System" is shown at the very top of your list of disk activity, sorted from highest usage to lowest. Mind you, this does not always happen, but it's not all that unusual, either. I just tried opening Task Manager because I'm accustomed to getting that brief "blip" of very high I/O activity upon doing so, but wouldn't you know, not this time.
If you return to much lower I/O throughput percentage within a few moments, sometimes as long as 30 seconds, but usually less, I wouldn't get too concerned about it.
If you've got a consistently really high percentage, then look at the things at the top of that list (when you've selected the Disk column and have it sorted in descending order [the little chevron will point downward]) to see what are the I/O hogs and then try to determine why. You will always experience periodic spikes in disk activity and it is not unusual to hit 100% for a few brief moments, but it shouldn't stay there for long [unless you happen to be doing something disk use intensive, such as a antivirus full scan or antimalware scan of your disk drive].