To cover a water stain on a popcorn ceiling, cover the stain with a stain blocking primer. It may be necessary to put on more than one coat. If the ceiling was painted before, you will need to repaint over the primer.
Covering up the water stain is likely to be messy, so be sure to wear a face mask. The stain blocking primer usually comes in spray bottles and spraying it on will work for a small area. If you need to cover a larger area you may want to consider rolling it on. If you need to repaint the ceiling with an original color then you should purchase oil based or acrylic paint. Popcorn texture ceilings tend to absorb water based paints, which will require more paint.