I was able to create three identical water profiles and delete them through Ingredients > Water > [highlight profile] then either right click/delete or use the delete button. However, in each case I changed the name of the profile so they were not exact duplicates.
If you are trying to delete through the Add Water or Substitute Ingredient buttons, deleting is not available.
I did sort of replicate the issue by opening BeerSmith via documents/BeerSmith2/water.bsmx. Deleting the duplicate profiles in that view was ineffective as they returned when I opened BeerSmith normally.
Have you tried deleting any other ingredients, like malt or hops? If you have a similar issue there, I would suggest reinstalling BeerSmith. It may just be that something became disengaged.