"butelkę wody" and "szklankę wody" would be Accusative of "a bottle/glass of water". Like "poproszę szklankę wody" or "Kupuję butelkę wody".
Here, you have quite a different situation. "a glass with water" would be "szklanka z wodą" (Instrumental), but that's also not that. Here you fill the glass with water. You use the water as an Instrument. So it's bare Instrumental without any preposition.
Thanks, there as I've said so many forms of expression in English that don't translate well in other languages. That and the instability of English, every time you turn around, someone changes a word or a sentence, we are in a constant state of flux. Small wonder my have a difficult time understanding us, including the British, the mother language.