Two thoughts:
as you know the edging stones are normally mortared to the lining. *So when
the pond level is low you can simply brush onto the liner a wet mortar mix.
This will change the colour from black to mortar colour which will then
green over as it becomes mossy. Don't get the wet mortar into the water cos
it might harm the fish.
Secondly, is the slope of the liner such that you could cover the liner with
gravel?

Davy

...

Interesting thought about the mortar. That could work.

The angle is mainly steep. At a couple of shallower points we've been
able to pile up some attractive pebbles to conceal the liner but this
doesn't work for most of it.

Will