"I do not have water."
Why do we say Nemám vodu but we say for example Nejsem holkA and not Nejsem holku? What is the difference, aren't both the verb reference?
In one sentence it is the subject and in the other it is the object. Therefore they have different cases. The sentences you show are very different in fact.
After doing my researches, it seems that it's just that the verb to be is non transitive, as they both are the verb complement
One is the subject and one is the object. When you say I am a girl, girl is still the subject. It's the same as I in the sentence. When you say I don't have water, water is the object that I has. Therefore the different ending.