Learn German: Geh schnell runter!

It is the colloquial, shortened version of either hinunter (down, away from the speaker) or herunter (down, towards the speaker). In everyday spoken German, people often drop the hin- and her- and just use the r- form, which conveniently means you do not have to worry about the speaker's location!

Is runter acting as a separable prefix here?

Yes! The verb is runtergehen (to go down). Just like other separable verbs, when you use it in a command like this one, the prefix (runter) separates from the main verb and gets kicked to the very end of the sentence.

Could I say Geh runter schnell! instead?

No, that would sound very unnatural. Because runter is a separable prefix here, it has a strict grammatical rule: it must go at the very end of the clause. Adverbs like schnell (quickly) must come before the prefix.

Why is the verb just Geh without any ending?

This is the informal singular command (imperative) form. When you give an order to someone you address as du (you, informal), you take the present tense form (du gehst) and drop both the pronoun du and the -st ending.