there is one way of creating artificial 3d photos underwater, or overwater, with only one camera, one lenses:

• take one picture, not too close, not too far. subject Ideal distance is min 1 meter to 10.
• try to take picture of something big, non moving, like a big boulder of coral
• try not to take picture of fish or moving subjects when shooting with only one lense (very hard to get proper parallax shots with only one lense)
• after the first shot, keep all the settings of the camera the same (keep settings in manual mode)
• then move HORIZONTALLY away slightly, then take another picture of the same subject
• why? vertical deviations are not easy for the eyes or the software to compensate. your eye muscles can compensate to a certain degree shifts in horizontal deviations, but vertical are a lot harder for the eye muscles.
• for the 2nd shot: you will want to keep a slight “convergence” : try to slightly shift the camera in an imaginary arc compared to the first shot. Your eyes are more capable of converging than diverging view.
• try to keep the main subject centered on both shots
• the idea is to shoot the same subject with a slight horizontal deviation difference between the both 2 shot
• And of course, underwater shots will be extremely harder to just shoot a horizontal deviation, without introducing a vertical deviation.
• then at home. with a software called stereo photo maker, you can then combine both picture into one 3d  http://stereo.jpn.org/eng/stphmkr/
• if the subject is further, more horizontal deviation between the 2 shot is required for greater 3d effect.
• it is artificial, so results vary a lot. YMWV

i have not tried it underwater, as i have a true 3d camera, but if you have two pictures of the same subject, whale, mantas, etc, you can try to create a 3d image for fun. a “true 3d” camera function on the same principle, 2 shot with a slight different view horizontally. It is a lot easier as the shots are taken with fixed deviation, and at the same time, same settings, synchronized. The problem with the current 3 d camera photo is: they ahve problem converging, or changing easily the convergence settings. They can change the artificial axial difference settings, but the convergence and focus at something close up is harder to adjust in current 3d cameras.

MACROS shots:

• with 2d macro shot underwater, pro photographers tries to blur the background, or use a black background to keep the subject focused and your brain focused on the subject. less distractions
• In 3 d world, your brain unconsciously  blur the peripheral details or background details  when you try to focus on something very close. The issue with the 3d camera for macros is that everything is still clear, from far to close, center to periphery. hopefully the future generation of 3d camera will allow more creative defocusing
• in 3d movies that you see in cinemas, for close shots, they try to use similar technique: keep the main subject focused on both right and left eye, in the center. While the periphery or further background is blurred.
• a good 3d picture does not have too much vertical deviation between the 2 shot, the 2 view. Shooting 3D macros subjects of pygmy seahorse resting on a background (sea fans) is extremely hard, as with most view, you will introduce a vertical deviation.
• Unless you can position yourself to directly view the macro subject  in a relative DIRECT view where there is not much sea fans introducing a vertical deviation, and where the main focus subject is in the center, not much distracting background around it, like in the next picture:

if you can have a macro view like the one above, then 3d macro is possible. The idea is to make the main subject look like a 3d “island ” and pop out, closer to you then the rest of the background.

the picture below is a picture where 3d macro is harder : too much background, foregoround,  and oblique sea fans introducing vertical deviations