You could check the SMART status of the drives.
One more idea is to make a note of what file you were watching or what file was being written when you hear the noise. Normally drives will turn off after 30 minutes of non-use (this is the Windows default) so you will know that most likely on the OS drive and the drive on which the file you're working with is located are spinning. With enough data you can probably narrow it down to a specific drive. Of course if the drives are in RAID then this will not work.