Slow HDD, Need resolution fast!

Hey, Recently my hard drive has began to deteriorate in speed so I decided to reinstall windows onto a spare HDD but once I had done this and tested the speed on this spare hard drive - which is normally better than my original hard drive - it had also dropped significantly. It seems whenever i'm booting from either drive the drive not in use drops in speed as I tested the speed once I had booted from spare hdd and tested my supposedly deteriorating disk and the read speed had changed from 3.0 MB/s read speed to 100+ MB/s read speed and this also happened when I booted from my deteriorating HDD and tested my laptop hard drive which was 3.0 MB/s when I was booted on it but when testing from my deteriorating one it was 90 MB/s+. Could somebody please tell me whether it's my HDD's or my motherboard or something else.Thank you very much for any help :) 

Maybe try different sata ports - even on a different sata controller as well.

Also check your BIOS and asscociated motherboard drivers - sata etc are all up to date as well.