It really depends on what you are accessing. This is precisely why copying thousands of files across locations is slow (have a look here).
Thus, if you are actually performing operations where you need to access files spread across the hard drive, you are going to get much more utilization even when the transfer speed is actually very low, and in other situations where you have contiguous data, you will have much lower utilization of I/O even with higher speeds. Thus, it is all about what operations you are performing.
Another reason, as it has already been mentioned is that the disk could be heavily fragmented, and thus to access any file, the disk will have to spin much more for accessing the same data. Thus, my suggestion would be to defragment the drive thoroughly.
If this doesn't work, you can try a reinstall of the OS, since it could also be malware.
The final reason, again as mentioned before, could be a failing drive, in which case you can't really do much. Try checking it for bad sectors and such.