lets start by tasting the water.... fresh or salty?
if sea water, then you get dish washing liquid and whip the whole inside with soap bubbles, and look for the bubble maker.
Bubble up the hose that run thru the transom to the tabs and the screws that hold them
you are taking about the little tube, that cuts thru the boat Stringer RIB to let the water drain down to the engine bilge.
If you not seeing the water around the batteries, then you need to get a pick and poke your RIB stringers to see if they are water logged or rotten.
Sounds like you have a hole and it could be in the transom, and the water running under the gel coat and into your boat.