The answer is no. An Bord Pleanala can not be over ruled by the County Council. (Of course it would depend on what is being retained , why it needs retention and how it contravenes an An Bord Pleanala edict / condition.)
If there is a complaint under investigation I'd suggest you complain in writing too, as this would strengthen both complaints & may help the Council's Enforcement action.
You must also understand that their is no way the Council can know that your water has been poluted, unless you test your water & give the results to the Council. You may also need to show how your neighbour is responsible for poluting your well.
I think you need to retain a professional to advise you on your particular case. It is difficult to advise here when one is unfamiliar with all the facts.