[Lonthego]

は and が is truly the bane of Japanese language learners, even those who have been studying for years..the problem is that if a Japanese textbook were to introduce all their nuances and uses, it would turn beginning students off and they might be discouraged and confused.

In terms of what you have learned so far, there COULD be は instead of が when using あります and います, especially if we are talking in terms of contrast.
You wrote 水がありますか
If you asked that, I could reply 水はありますけど。。
I have water, but..(I don't have a glass)
It's showing contrast, you do have X, but not Y..it's hard to convey in writing because in English we express this by intonation and stress, not actual words or particles.

Or you could say タバコはありますが、火はありません (or ライターはありません） I have a cigarette, BUT I don't have a light
火 = a light in this context, like we say it in English

Or you are at a party, you ask a friend if Mizuki and Ken are here, that friend might say
みずきはいるけど、けんはまだ来てないよ Mizuki is here, but Ken hasn't come yet

を can be replaced by は as well to show contrast. Showing contrast is just another huge part of the whole は が fiasco that has to dealt with..but there's no need to learn it all at once, you can pick it up as you progress. To avoid confusion most textbooks I think do not introduce both Xがありますか as in asking if you have something and also using は to show contrast at the same time, so maybe it's in another chapter or something.