If you want to use a preposition "by" is fine. He crossed the creek by using a tree as a bridge. In your sentence you really need a comma between "creek" and "using".

How about "via"? He crossed the creek via the fallen tree. (This tells us a few things... first, perhaps there were other ways to cross the creek, even if it included wading across; also, "fallen tree" makes it clear that you could use the tree as a bridge and that you didn't need to climb it!) Hope that helps! :)