Re edging a pond, you might like to browse the following pages
http://tinyurl.com/pmra4
http://www.koicymru.co.uk/const12c.htm
http://www.koicymru.co.uk/const12a.htm

As a quick answer I would say that providing you let the cement set (3
days or more) before there is any chance of residue being washed into
the pond and that once it has set you scrub and wash off the surface
and vacuum out the washings then you dont really have that much to
worry about. That is especially true if your water is alkaline anyway.
Why? because the exposed surface area of the cement isnt large and once
set most of the alkali is within the body of the cement. Note however
that it would be better if the flagstones also slope away from the pond
so that rain water doesnt run off the paving into the pond.


That said I personally would most likely cast an at least 4" deep x 9"
wide concrete collar around the edge of the pond as a foundation for
the inner edge of the flagstones. Once that had set I would trim the
liner flaps to about 4 to 5 inches in width and then dry layout all the
flagstones. Then lift the flagstones and put about 1/2" of cement on top
of the collar, whilst the cement was soft drape the liner onto it. Then
I would immediately lay the cement into which I was going to bed the
flagstone and that includes over the liner flaps and bed the flagstones
into that cement.
Why go to all that bother? It gives the pond a solid edge and the liner
cement sandwich protects the liner. Things to watch for, cement
extruding into the pond, that needs to be vacuumed out asap. Also that
no extruded cement ridges and formed between the liner and the side of
the collar. The latter could be prevented by covering the say the inner
1/2 to 1/3 of top of the collar with a strip of plastic sheet which
projects into the pond BEFORE the cement is applied to the collar. Once
the cement is laid on the collar and over the 'edge' of the plastic, the
plastic is folded back over the cement and the liner laid in place. Trim
the plastic to match the liner flap and proceed as before.


--
sean mckinney