I use my knowledge of flora and fauna to start me off with the magical world's equivalent and then research what I don't know to work out how magical creatures could be different. It's not just a question of a dragon being able to breath fire or knowing they like meat!
One of my dragons in The Trouble With Mother strikes Eileen as being different because it doesn't rush to attack her or Hanastrew. (Most dragons would take the chance to kill anything that might threaten them or would make a tasty meal and in this case both of those things would apply). So sometimes knowing what would be unusual behaviour for an animal can be useful in storytelling.
Working out what could threaten the landscape in your fictional world can be an interesting avenue. I've used magical wars to make the land barren in places on the grounds nothing can stand having too much magic go through it in one go, which I think is a fair enough conclusion. This gives me history to my fictional world (which to date I've only touched on lightly but I hope to come back to this in future books). It also gives me an "ecological" aspect to my fiction and a reason why Eileen doesn't use magic unless she has to (and that most responsible magical beings would take the same view, not wanting to cause further damage and recognising the harm that has been done).