What might be your concern? The nails will rust away and the liner will no longer be held in place or that the rust will harm the fish? I don't think there would be any concern with either of those ideas.
I would just leave it.
You mentioned galvanized nails.
I have read that galvanized products can be harmful to fish due to the zinc content. But I don't see how a few galvanized nails could even be a factor with so little material exposure.
So, it's up to you.
You could pull the nails if you like and run a bead of PL-S30 adhesive under the liner. It's a polyurethane based roofing adhesive that some members here have used with good results. It comes in tubes for use in a regular caulking gun.