Without knowing what he's like all the time, it's difficult to say whether you should be thinking of leaving or not but it does sound like this is something that has built up. He hasn't seen the problem, but every time it's been niggling you until you snapped. He should have paid attention to you earlier, but it got to a point where it wasn't 'just' the water, it was months of you feeling annoyed and him not listening to you, so it became about more than the water.
So water is going to be a bit of a sticking point at the moment, because both of you feel that the other is being completely unreasonable (personally, I agree with you that he should get his own).
So, I'd change the system entirely.
You're cooking, he sets the table — he could get your DD to help if you all eat together? It's a good chance to practise counting knives, forks, spoons and glasses. Also, give everybody the same glass! In your twenties you don't need to have favourite glasses. Then, put a jug of water on the table, and there won't be a problem.
With that removed (because honestly, at this point it's clouding judgement for both of you — you feel resentful, he feels got at), you can see what he's like the rest of the time.