Sure.
Just one thing to be aware of:
Since POP3 does not provide read state sync, it's common for mail services to mark as read any message that has been fetched over POP3.
And then, since IMAP does provided read state sync, you'll be getting those messages as already marked read in AquaMail.
Some mail services have a setting for this, some don't and still do it.
Your best bet is to test it yourself, maybe having web mail open so you can monitor for read state changes.
Oh, and one more thing - if this is a Gmail account, please read this:
"Using POP on multiple clients or mobile devices"
https://support.google.com/mail/answer/47948?hl=en
