I'm still at the phrase of translating individual Russian words into English equivalents and saying it as Pidgin English to get a translation... so I thought this said "what eats a fly?" - as in which creature would eat a fly.
How would you say this? Is it achieved through declension endings, like in German? Or word order?
This sentence can mean both "What does the fly eat?" or "What is the fly eating?". We cannot know without context.
If you want to be precise about this in Russian, you can add some extra word to clarify. Personally I would go with something like:
что (обычно/всегдо) ест муха? What does the fly often/always eat?
что ест муха сейчас? What is the fly eating now?