How to humanely kill a fish?

I have a dwarf puffer, had her for going on six years and two days ago she did not come out to eat her worms and then I saw her and she is sorta on her side and has a pea sized growth on her side (which is quite large on a dwarf puffer). I am sure she is near the end of her life but I have a problem flushing a living fish even if it is dying. Any suggestions?