How about simply not permitting this situation?
I don't know how you are making your game, but if you detect that the view will be partly underwater, you can force the camera to be above water, and only when the entire view would be below water, you can switch to the underwater view.
Depending on how you do it, this could mean that there is an additional delay from the moment where you start diving and when you actually view the scene from beneath the surface. This may actually be a good thing from a UX perspective, so feel free to experiment.
On a separate but related note, I wonder why most underwater scenes are rendered crystal clear... If you ever put your head underwater, you will notice that your eyes are not designed for underwater sight, and therefore everything seems blurry. You'd have to be wearing goggles to actually see clearly underwater.
And additionally, things look (and hear) very different underwater than above water. Water absorbs light much faster than air, so the farther light travels, the less light will arrive at your eyes. This means that the deeper you go, the bluer things look (red light has less energy, and is therefore absorbed more easily than blue light). In fact, at a mere 12 meters underwater, blood looks black, not red.
I've yet to see a non-specialized game that even tries to get underwater environments right...