Well I’ve got some bad news ;-{
This macOS version don’t work well on HDD’s as it runs the newer APFS file system and currently there is no means to defragment the HDD like we could with HFS+. It was designed to run on SSD’s which work on a block basis not cylinder/sector a HDD works off of.
So to fix this you will need to backup your drive (TimeMachine), then reformat it and install a fresh OS onto it and then restore your user accounts, apps & data (Migration Assistant).
The other approach is just bite the bullet and get a SSD swapping out your old spinning rust drive.