There are OS processes that have to execute at specified times, such as overnight. If your Mac is sleeping overnight, the OS will execute the processes after waking up.
However, when this happens again, take a look at Activity Monitor and sort by CPU usage, descending. It'll show you what's dragging on your system. CPU doesn't equal disk activity, but it often correlates. If you let us know the processes hogging CPU, we can offer some more detailed insight.