You can control here, globally for the whole instance, the use of notifications. By default, all these options are checked.
Any user can personally specify via my profile if she desires to get daily or weekly emails with all outstanding notifications.
If your browser allows notification, Matrix notifications can appear as browser notifications to make sure you see it directly if you're on another tab than Matrix for example.
Note: this feature can be globally disabled in the server setting for notification by setting in the advanced