That's accusative vs. genitive problem. You can use either accusative or genitive in a such sentence with slight difference in the meaning. There is additional complication. Some nouns have the special form of genitive which is called partitive. "Вода" doesn't have it. You can see partitive in action when you hear "сахару" for example. There are three possible variants:
Хочешь сахар? - accusative. It refers to a substance as a class. Соли нет, хочешь сахар?
Хочешь сахара? - genitive. One of the multiple functions of genitive is to refer to some amount of a substance: "стакан воды", "ложка сахара".
Хочешь сахару? - partitive. It's the special form of genitive to refer to some amount of a substance: "ложка сахару".