I realized in hindsight I probably should have saved, and then come back to take a screenshot of Naija going through the rocks. If she swims against the ceiling there, she can slip through the boulders, which I'm pretty sure she's not supposed to be able to. I got into the tunnel without any problems, but getting back out I did have a little bit of trouble. Eventually I switched to fish form and found the gap that let her through to get back out (whew, or else I would have had to restart from the last save).
This is in Open Waters, coming from the Veil. I guess the Ekrit helps locate it.