flood underneath my liner

Well, I thought I was so clever moving my waterfall to a better spot on my
pond, but imagine my surprise when I came home (with 2 new koi) to an almost
empty pond. Yes, I had not checked the placement of where the waterfall
was coming out well enough and it was dripping back behind the liner causing
it to lift up in several spots and empty out the pond.
So I'm filling the pond back up with water and plenty of declor, but
will the water that is under the liner eventually soak into the ground so
that I won't have these raised spots forever I hope?
Kirsten