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I assume by 'watermark' you mean adding something that will uniquely identify the version of the ePub that you distribute. What purpose do you want the watermark to serve? If you're preparing several different versions of an ePub to send out to different people, then the most obvious route is simply to change the <dc:identifier> value in the content.opf file. Obviously anyone can edit the ePub and change that, but they could change any code you add to the text as well.
If you want to obfuscate the watermark so that it can't be easily detected or changed, then that's a different issue, but is quite possible with some technical skill. Most ePubs contain one or more images and there are several ways of watermarking a jpeg.
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