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So, the reason the whole alignment of the cpl to a water reflection and then to something else method doesn't work is down the geometry of the situation being changed when you move the camera - as stated above .
Polarisation by reflection is what everyone sees when improving foliage saturation on wet days and removing reflections from water surfaces - Essentially anything that is a dielectric (not a metal or a semiconductor). Dielectric surfaces (lets assume a flat surface for the sake of ease), at any angle other than zero degrees to the surface and 90 degrees to the surface, preferentially reflect light whose electric field oscillates parallel to the surface of the reflector more than light whose electric field oscillation has a component which is perpendicular to the plane of the surface (respectively, these are known as S- and P-polarisation states). For anyone who is interested, look up Brewsters angle, 'Fresnel reflection' at a surface, and salient terms therein such as 'dipole scattering. As stated above also, a "circular polariser" in photographic vernacular is a linear polariser followed by a quarter wave plate. The latter component is what circularly polarises what ever is passed by the linear polariser. So, arriving at the point, the reason why reflections from water are reduced, is because the flat dielectric surface of water preferentially reflects light which is S polarised (Linearly polarised parallel to the plane of the surface) and the linear polariser at the front of your circular polarising filter can simply be angled to cut this out. For those that are really interested, the physical reasoning behind all this is down to the asymmetry in the environment for the very top most surface molecules.
The atmospheric effects that can be seen when using a cpl, especially in blue sky, is caused by polarisation by scattering. The reason the sky is blue is because of a process called Rayleigh scattering. This scattering effect is typical for particles much smaller than the wavelength and it just so happens that the composition of the upper atmosphere is the right constitution of matter to predominantly scatter blue light. I won't go into mega detail, but polarisation of this light is caused by dipole scattering - it dictates that if you are stood in an arbitrary position and a light source exists so as to cast light directly across you, any scattering particles in front of you will preferentially scatter light towards you that is vertically polarised, not horizontally. This is the same reason why mast antennas are stood up, not horizontal. This is also the same reason you get the dark blue area of the sky only at 90 degrees to the sun when shooting the sky with a cpl. However. And yes there is a however. The magnitude of this effect is dependent on the concentration of scatters - the number of times light is scattered before reaching the observer. This is partly the reason why clouds are largely unaffected - the other reason is to do with the particle size in clouds. Haze is typically made of water vapour on humid days, pollution and other stuff - particles much larger than in clean, dry air, and so this same polarisation by scattering does not have the same effect. As such it's not likely a CPL will do much to cut through haze. (I'm not saying it wont have any effect at all, simply that it'll be significantly reduced.
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