Well, it all depends on what you are trying to accomplish.
In a conflict, the water zones can be given a high border value, making it harder for people to move along, while aquatic characters can ignore that.
I guess for drowning a good rule of thumb could be endurance. You can hold your breath for endurance exchanges, after that you get 1 shift of damage per exchange, that can't be resisted.
For fighting in water, you could add a flat armor:2 for everyone, that aquatic characters can ignore, to model the increased difficulty to move and fight.
Sometimes, it might be a flat out compel or a way to refuse a compel without paying a fate point. "No, you can not walk to the ground of the sea to get the artefact. Oh, you have the aquatic power? My bad, go ahead."
As Harboe said, it really depends on the situation, and if it warrants complex rules or if you can handwave or solve things with a single roll.