To be dead in the water means to be completely defunct, and in this sentence the person is wondering how things would have gone if they had found the other person not functioning.
Consider the staetement "Watching her now, I wondered how things would have gone for me if I had found her not functioning or moving at all instead.". Based on this statement, is "Watching her now, I wondered how things would have gone for me if I had found her dead in the water instead." a true statement? Yes/no/unknown