Salt water in your swimming pool attacks your eyes through the process of corrosion in two different ways. First, the salt itself in the water attacks the sclera (the white of the eye) and the cornea (the clear dome at the front of the eye). Then the chlorine in the water (which is generated by the salt “system” on your pool attacks the same parts of the eye. One recent study out of China found that the damage of chlorine to the eyes and skin is much more significant than previously thought and this will hopefully lead to more studies on the subject.
Alternative sanitation systems such as the Drinkable Pool Water System are a much healthier choice for modern pool owners but they can be a bit pricey.