If the tree isn't watered, it (will die - dies - would die).
I know zero conditional should be about facts. In the example above I'm confused whether to choose will die or dies.
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Both will die and dies are grammatical.
In normal speech, you would use will die; but in present-tense narrative (for example, in a documentary film) you might hear dies.
It should be it dies because zero conditional refers to general truths. It is clear that your sentence is zero because watering trees a scientific truth.