"A completely submerged creature has total cover against opponents on land unless those opponents have freedom of movement effects. Magical effects are unaffected except for those that require attack rolls (which are treated like any other effects) and fire effects."
"The surface of a body of water blocks line of effect for any fire spell."
So water doesn't block line of effect, except for fire spells. And spells that require attack rolls cast from outside of the water do not effect someone completely submerged in water, because that individual has total cover.
Aqueous Orb specifies that it provides cover, not total cover. So it just provides an AC bonus. But the surface of the water still blocks line of effect for fire effects.
