can be 2 things imho:
1. It can be something like some adware you installed. Try to scan with http://www.herdprotect.com/
2. Check your extensions in your Google Chrome browser. Disable extensions (one by one if needed) and see if i gets rid of the adds. (Check if the pop ups happens on all your browsers or just chrome.)
If all fails, revert to a previous backup or reinstall Chrome after backing up your personal data to an external drive. Good luck.