Aside from what TheSlider all correctly surmised, (It can either be HDD, cable, or RAM) and the slow-down is when errors cause windows to disable DMA modes for that drive, and switch it to PIO (which is INFINITELY slower)
There is also the possibility of Malware infection causing these issues. However unlikely, but I would suggest looking at the task manager (Ctrl + Shift + ESC) to see what your CPU usage and RAM usage is during idle and if all fails, scan with AV (or Spybot, Malwarebytes etc.)
You can never know for sure what exactly causes an diffuse issue like the one you describe. What HDD do you have, did you check (and replace) the cable in question? SSD or HDD, etc.