If i had to guess i would have to say that your drive is fragmented and so the hard drive has to work a lot harder in puling up the content that you requested. Try to defragment the drive and see if that helps.
Yes, fragmentation is probably one of the problems. The other problem is you should ALWAYS leave at least 10% of the drive free. Once you start to fill it up beyond that, the drive doesn't have any buffer space for when it's reading and writing at the same time.