Bear in mind adding watermarks is a rather intensive process depending on the size of the watermark and the size of the image.
You may find it a struggle to do more than a large amount.
One workaround, is to increase the number of media items per page, then use the inline moderation where you can then select all on the page. Your selections are remembered across pages, too. It will take some time, but that's the only solution at the moment.