Translation:We do not have food, but at least we have water.
It's how the phrase "at least" is functioning. When it comes before the entire sentence, it modifies the entire sentence to mean something like: (thank goodness) at least ...
When it comes at the end it is at best ambiguous what it modifies, however, it would attach itself to the closest thing, though English doesn't grammatically function well in reverse order, minus question sentences. Therefore, it'd mean something like: we have water, though we might have something more.
The context of the grammatical structure want to convey that they don't have food, and we don't know that they have anything else except water. Word order is proper and necessary in English, and most other languages when you get down to it.