I recently bought an SSD and installed Windows 10 from scratch. As soon as I started configuring Windows I noticed that my HDD, which housed the OS before, started making constant clicking noises, similar to those you get when copying random files from one partition to another but even louder.
I reinstalled Windows a couple of times to get it to have the drive letter C. When I finished, there was no clicking noise at all so I relaxed and forgot about it.
I backed up all my files off that HDD and used DBAN to clear everything out because I wanted to merge all my partitions but there was a small partition in the middle that even EaseUS couldn't do anything about. After creating a clean partition (it's a 1 TB HDD), the problem reappeared, it was making the same continuous clicking noises.
The funny thing is, it only makes clicking noises when it's not being used at all. As soon as I create a single folder or file on the HDD, the noises stop. Once I stop doing anything on the HDD, the noises start up again after about 10 to 20 seconds. Hard drive's activity is 0% whenever those noises appear. Even when completely formatted, the head still sounds like it is searching for something. Copying files makes much less noise.
I tried lurking in the UEFI to see if I could find something, and I noticed something: the HDD was making the same noises inside the UEFI.
The temporary solution I found is to set the HDD to stop spinning after 1 minute, since it only makes that clicking noise when it's not being used, the hard drive stops spinning and turns off after 1 minute.
I have a strong case of misophonia in regards to repetitive sounds, so the clicking pattern it makes drives me completely nuts. Even the 1 minute I have to endure borders torture.
TL;DR: empty HDD makes continuous clicking noises with 0% usage but stops making noise when it's being used.