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.
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.