Rangersedge,
I'm no geologist or engineer & I don't play one on the internet.

I was waiting to see if someone with experience would respond. But I do have an opinion.
If it were mine I would have to remove the topsoil. I would have to know what I was dealing with. The topsoil, unless it is clay shouldn't be able to contain the spring if it is very strong therefore the soil around the spring should be saturated. If not it must be a small spring at the point of entering the topsoil which will hopefully be easy to seal and I would rather not have a layer of topsoil between the spring & my clay liner.
Just my opinion ...
Ric