I think it is actually easier to poison a well than pollute a river. Especially a fast moving river. I believe there are plenty of historical stories of a castle's well getting poisoned by tossing infected meat/rodents/etc. into it. I guess if the invaders down have access to the wells or water table those would be safe.

You can add fell-beasts or other monsters that inhabit the mountain, environmental conditions, or just the logistics of dragging an invasion force over it. If whatever passes are there, are easily defended (a la the movie 300) that would discourage a large invasion as well.