OK now that we have the information you can use this:

http://docs.unity3d.com/Documentation/Components/class-WorldParticleCollider.html

that you place on the water. Read it through to know what to do (exemple, enable Send Collision Message)

Then

function OnParticleCollision (other : GameObject) {
    if(other.tag =="Fire_tag"){
        Destroy(other);
    }
}

Add a collider box to your fire, tag your particle system with Fire_tag (or else) and you should be good to go.

P.S: I do not have Unity to try it so I might have missed a detail...

Colliders will do it. I dont know how the fire and the water will be featured in your game, but basically you could add a collider to the fire prefab and check if it is hit by water. If you use colliders or cast a ray, sphere or whatever against it depends on how youre going to implement it of course. Then, if hit, simply destroy the fire object and the fire is out.