I'm using Fedora and day by day my system's performance gets worse.
Can anyone tell me what might be causing this and how can I fix it.
This program will show what the (hardware) bottleneck is in your system.
Press "D" to show which processes are accessing the disk, maybe a service you don't use is degrading disk performance.
Before the edit, you mentioned a concern about temp files.
Temp file are often deleted when a system is rebooted.
I don't know if this applies to Fedora, but you should try rebooting, if you haven't already.
Another explanation may be that the HDD is slowly failing, such that retries following seek operations are becoming more common.