"A glass of water"
Translation:Ett glas vatten
Not at all, you're conflating grammatical gender and "natural" gender, when the two actually have little to nothing to do with each other. If the word "gender" concerning nouns bothers you, you can also remember it as all nouns being in one of two categories: "ett-words" (commonly referred to as neuter gendered nouns) and "en-words" (common gender nouns). When you learn a new noun, you have to learn in which of the two categories it is. Here, it is "ett glas vatten" because "glas" is an ett-word.