God didn’t have enough water at his disposal?
Well, there is that.
The planet as a whole was caused to contract, a simple heart beat, if you will.
Thus, the water levels being constant, one can imagine how a contraction of the actual land mass would cause the entire orb to be covered in water, then when the land mass expands once more, voila, there are fish and horse skeletons everywhere.
neat, concise, covers all the facts...elegant.