It can be as little as damp wiring to as big as hydrolocked pistons.
Remember, water doesn't compress so it bends whatever is trying to compress it. The air intake is pretty low on those 8th gen civics so it can well be the latter. Check your airfilter and if damp replace it. Remove your plugs and try cranking the engine, the water should be thrown out if there is any inside. If you can't feel any new knocking sound, you are probably safe. But its always better to get an expert opinion.