Rob E's excellent answer covers the case where the application can (and the user wants to) mark specific passages of text.
If you also have (or want to offer) a simple "bookmark this page" option, without the user needing to mark a specific passage, then I think you should store the "location" of the paragraph at the top of the current page. When returning to the bookmark, display the stored location at the top of the new page.
My first instinct was to suggest storing the location that's closest to the middle of the current page (with the reasoning that if you put that bit of text in the middle of the page when you return to a bookmark you would be "reasonably close" to where the reader wanted to be, most of the time, for most zoom levels).
However, as an avid Kindle user, I thought about when I use the bookmark function as opposed to highlighting a passage of text:
If a work of fiction has a map of the area where the action takes place, I'll often bookmark that page so I can return to it easily if I need to check the geography.
If there is some kind of glossary, list of characters, ... list of almost anything, I again might bookmark the first page of such a list so I can return to it easily.
The common thing is that the thing I'm marking is usually either the only thing on the page (very often the case with maps) and/or forcibly starts a new page (usually the case with glossary or similar). In both cases, going back to the beginning of the page originally marked seems to be the correct thing to do.
Also, as Monty Harder pointed out in a comment, when using a bookmark for its "traditional" purpose – going back to where you left off reading – then bringing the text that used to be at the top of the page back to the top of the page (even if the zoom-level is different) is the safest option: at worst, you might have to skim over some parts you've already read. However, if you brought what was in the middle of the page back to the middle, there is a chance (if the zoom-level has increased) that unread portions of the text have been pushed back on to the preceding page.