Hey there, RagingRabbits.
@bgunner is right, the beeps are most probably coming from the speaker connected to the mobo. As for identifying the issue, first you should backup your important data, just to be on the safe side. After that, go ahead and download the HDD manufacturer's diagnostic tool and run the tests, to see what's the situation with the HDD. Please let me know how it goes.
If everything seems fine, you can try it out with a different SATA port and different SATA cables (both data and power).
If there's no problem with the HDD, answering @bgunner's questions about the beeps could prove useful. Other than that you could run a system stress test to see how your other components perform.
Hope that helps. Please keep us updated.
Boogieman_WD