? Have you run any virus scans and come up with any troubles ?
There are too many programs out there to list that would fly under the radar of an antivirus, but require the other person to have physical access to your computer to install a service. Did they ever send you anything to install or run, or have they ever had access to your system in an accessible mode to install a service such as if your computer is left unattended and logged on?
Most simplistic fix if you cant target to remove the software or service would be to back up your data to an external drive and restore the computer back to factory default. Then be sure to set a password on the system and a screen saver with a lock to lock the computer after say 5 minutes of inactivity. This might be a pain as for if you walk away to get coffee and more than 5 minutes pass you need to enter your password to get back to whatever you were working on, but its the most secure method with a questionable flatmate causing troubles.
Additionally they might not have anything installed on your system at all and are just sniffing the wireless with a tool that watches packets. They can see traffic to and from your devices and know where you have been based on IPs and any unencrypted data transferred in packets. So if this is the case, you will want to lock them out of your wireless network if they are on it. This is a wireless router config change.
Lastly how do you know they accessed your internet activity, are they sharing information as a threat or something else that gave you hints that they are snooping in your private activities?