Create a transparent PNG watermark image (eg: something that says Copyright Yourname with your logo).
Go to the Downloads > Settings > Extensions tab in WordPress.
Upload the watermark image using the Choose Image button.
Select where you would like the watermark image to appear.
Create a New Download and upload an image. The watermark should appear on the image.
Note:If watermarks do not get applied after regenerating thumbnails, make the image paths relative e.g. /2012/06/watermark.png