Your usages are correct, in this case, it's very fluid, no pun intended. 'I'll have a mineral water.' 'I'll have mineral water.' 'Give me two mineral waters.' 'If I had to pick between the two mineral waters, I wouldn't pick the La Croix.' 'The store had a wide selection of mineral water (waters).' You can use either here. All the above are good, just don't pluralize 'waters' if your ordering just one, and you'll be fine.

Two bottles of mineral water please. (In this case only bottle needs to be pluralised) Side note reading the last answer. It’s common to mix up your & you’re. E.g “your order is ready” “You’re ordering two bottles of water?”