Why is this?

Technically, it's standing water. If a devil fruit user is knee deep in a pond or lake, they'll drown. But we don't see that since the only body of water around in One Piece is the ocean.

I remember reading the issue about water weakening a DF user somewhere, don't remember if it was in the manga or wiki though. What Exorcist said is technically correct but there have been scenes in the manga that confuse me. As far as the case of sea stone, i guess we'll have to wait until Vegapunk is revealed and explains it more seeing that he was the person that 'discovered' its effects.