water in case rough RIO LS 2005

have water in the trunk, even up to the back seats it has run. must have been a few months ago, since under the back seat of the foam at some places is black. it smells unpleasant and I just can’t get out. have removed the clothing in the trunk and noticed that the pinching of the outer sheet and the inner sheet the water in the 20 sec. clock runs when it rains. the best, it’s on both sides!!! I don’t know any more. who can help me????