The best option as a base coat to cover water stains on the ceiling is an oil-based, mold-resistant primer that blocks stains in a tone very similar to that of the existing ceiling. Oil-based anti-stain primers are insoluble in water, so water stains cannot be filtered out. You'll need an anti-stain primer, such as a simple spray stain primer, or you can paint it with a brush and roller. Our favorite stain blocking product is the Sherwin Williams Pro Block oil-based primer.
Another good product to use is Zinsser's B-I-N stain blocker. You'll also need flat white paint for ceilings, a ladder, cloths, an extension cord, safety glasses, a roller and a cover for painting, a brush, a tray and a liner for painting, painter's tape (unless you have a very firm hand) and good music to keep you motivated. If water damage is extensive and requires heavy lifting, you can use the KILZ Restoration primer. It is oil-based and can remove the toughest stains.
If you want to remove water stains from your ceiling paint, here's an article about the best water stain product for painting damaged ceilings. Knowing what is the best product to dye a damaged roof can be useful when you have another mishap. In addition, if you want to save on the costs of repairing and repainting your roof, try to check if water damage in your home is included in your insurance coverage. As mentioned above, the root cause of water stains must be corrected before attempting to remove them, and then it would be easy to remove water stains from damaged paint on the ceiling.