I am making coffee.When water boils pour it. = Pour the boiling water into or onto something.
When water is boiled pour it. - There's no indication of precisely when the water might have been boiled.
>>Which one would you use in a recipe?<<
Recipe for what? I don't think you would add boiling water to a cake recipe.
If you are describing how to make coffee, then "When the water boils, pour it into/onto . . . something (depending on the type of coffee you are making)."
Or 'When the water has boiled . . . ".
There's no difference in meaning.