Some badly written software leaks memory, and accumulated wasted resources can slow things down.
On machines which manage their clock speed and power, the system will also slow down if it starts getting hotter than is safe for the processor chip. But that's really more a matter of it being able to cheat a bit and run faster when cold.
Also, if your measurements depend on network transfer speed, it's not uncommon for ISPs to allow brief bursts of activity to run at full speed and then "throttle" your data rate if you start tying up a lot of resources for a longer time.
There may be other causes. To find out why you are experiencing a slowdown, someone has to look at your machine and how you are using it.
(Typos fixed.)