Is there any side effect/disadvantage to swimming; especially to the ear and eye inside a treated water?

Yes.: From the eye perspective, there are a variety of chemicals in treated pool water that can cause ocular irritation resulting in redness. My advice would be to wear swim goggles to minimize exposure. Rinse with a good artificial tears solution after swimming and you will minimize the chances of ocular irritation.

Yes: Repeated exposure to excessively chlorinated water (without googles) can cause a decrease in corneal stem cells which can lead to redness and dry eye in the future in some patients. Swimmers ear/infections in inner ear is well known to occur in certain patients who swim often.