Underwater Scene

For simulating underwater in stop motion, there are many options to help sell the effect.

A fogger or hazer is often used in dry for wet, but it can be too difficult to maintain an even saturation between frames for stop motion.  You can simulate fog by shooting through layers of scrim, breaking your scene into planes of depth, where the further back you view the more accumulative scrim layers there are for the captured image.

Lighting is key, so have plenty of references of underwater shots that are similar to yours, and try and match the lights using shape, color, and contrast.

For a more complex lighting effect, you can animate light shafts by using a cuculoris (aka cookie) to shape your light into beams that can be moved between frames.  Possibly having 2 layers moving in different directions in each frame.

You can also try simulating caustics, a refraction effect caused by light passing through the water surface.  You may be able to simulate this effect by shining a bright light through layers of textured glass, then animate it by slowly sliding one of the layers.

Adding in other animated elements like kelp/seaweed or bubbles can help, though that can be a lot of work for a single animator.

You can also add distortion to the camera to create a wavy effect by moving something translucent in front of the camera.  Either clear texture glass, a clear film, etc.

Some of these effects can be added in post, but with stop motion, it's usually ideal to capture everything in-camera.

That's just a few ideas off the top of my head, but I'm sure there is plenty more you can do.

/Chris