In a deep, heavy bottom pan, combine the granulated sugar and water. Stir together to begin to dissolve the sugar, trying not to get too much sugar on the sides of the pan. Run a clean pastry brush along the sides of the pan with bit of water. You want to be sure that there aren’t any granules on the edges while the sugar cooks (this can cause the caramel to crystallize).
Cook the sugar over medium heat, without stirring or agitating the pan. Watch the sugar carefully as it begins to boil. It will start out clear then turn light amber. At this point, carefully swirl the pan to evenly distribute the sugar and color. In a matter of seconds, it will turn a deep caramel color. Turn the heat to low and carefully pour in the cream. The pan will boil rapidly and there will be a lot of hot steam. Once it starts to settle down, whisk the caramel until it is thick and smooth, one to two minutes.
Stir in the flaky salt, then transfer the mixture to a heat proof jar to cool. Once the caramel is room temperature, transfer to a piping bag.