Assuming the cause of the water stains has been corrected and the lime plaster has dried out you could consider the options below. 

If the affected area is very small you could consider Graphenstone Four2Four, but please note that this can affect the breathability of the plaster. 

If it is over a larger area you would be best to try Graphenstone Ambient Primer L42, but this may or may not adhere to the water stained areas. 

Both of these if successful should be over painted with Graphenstone GCS Interior.

We would recommend to test on a small area for compatibility and adhesion prior to full application.