Help:Notifications/Popup documentation
Notifications Popup is a gadget that provides a "pop-up" badge on the top right of any WIkipedia page if you have any unread Notifications (as defined in your Notifications preferences). It was designed in response to concerns about the visibility of the new Notifications alert.
The badge will scroll off the top of the screen after a few seconds; clicking on it will cause it to scroll away immediately. It will continue to appear on each screen you load until you clear your Notifications by clicking on the red badge next to your username.
Though the gadget is ON by default for all registered users, you can easily turn it off by going to your Gadgets preferences and deselecting Display a popup when you receive a notification under "Appearance", then saving.