Light reflected from the water surfaces or smooth water is horizontally polarized.
This horizontally polarized light is blocked by the vertically oriented polarizer in the lenses. The glare from the water produces eyestrain, and can caused you to squint which can lead to a headache. Regular sunglass tinting alone can not cure this problem of glare from the water's surface.
Polarized sunglasses absorb the reflected glare and pass the safer light to your eyes which helps you see more fish and structure under the surface. You should use bands to slide on the sunglasses so you don't loose them over board.