There are two types of natural stone. Siliceous stone is made up mostly of silica or quartz-like particles and it's easy to clean. Calcareous stone is made up mostly of calcium carbonate. Onyx is a calcareous stone. Onyx is porous. This means if something is spilled on uncoated onyx it soaks into open spaces in the onyx and is hard to remove. Acid cleaners that are used on siliceous stone can damage onyx and other calcareous stone. If rust forms on onyx, you might need a professional stone finisher to get it out, but there are some methods you can try first if the rust stain isn't too deep.

1
Use naval jelly, which is made of phosphoric acid. It's available at hardware stores. Wear rubber gloves, goggles and a long-sleeved shirt. Apply the naval jelly to the rust and let it set for ten minutes. Rinse it off and dry it with a clean soft rag.

2
Apply buffing compound to the rust stain. Rub it with a soft rag to buff away the rust. You can find buffing compound at auto parts stores.

3
Make a poultice from a chemical mixed with a material that absorbs better than onyx. First, try mixing a cup of flour or baby powder with three tablespoons of dish soap. Use distilled water to dampen the rust spot and cover the stain with the dishsoap and flour mixture, Use masking tape to tape a piece of plastic wrap on top of the poultice. Leave the plastic wrap on the poultice for 24 hours, then remove it and let the poultice dry completely. Scrape the poultice off with a plastic scraper and clean the area. If the stain is still there, try a poultice made from a rust remover and diatomaceous earth, which is used in pool filters.

4
Buy Iron Out or another pre-packaged rust removing poultice powder from your hardware store. Mix the white powder with water to form a poultice. Mix it until it's the same consistency as peanut butter. Apply it to the stain, cover with plastic wrap, and leave it overnight. Remove the plastic wrap, let the Iron Out poultice dry , and remove with a plastic spatula. Clean the area and dry with a soft, dry rag.

5
Repeat the application of the poultice if the stain isn't removed. It could take up to five tries to get the rust out. After scraping the poultice off with a plastic scraper, try cleaning the spot with a cleaner such as MB-5 Marble, Granite & More Spray Cleaner and dry it with a clean rag.