Water and air have a different refractive index (different liquids will too, it is how oil is used for microscopy, to refract light enough at high magnification to allow focusing). Most shots I've seen along this idea have been with a fisheye, where the DoF is much greater and where the subject is closer. One in particular is of a lily above and below, although I have also seen one of spawning salmon with a landscapes in the background, but the landscape wasn't completely sharp from memory, it was more of a suggestion of the surrounding environment, just sharp enough.
Is there any way around this perhaps?
I'm using a 8" dome and a 15mm fisheye. Underneath the water everything looked like it was in focus with only aperture f4.5 in this picture.
Perhaps where you focus can have an inpact. Prefocus on a point a third into the picture?