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Water stains shouldn't be too difficult to remove - if they are not large or huge. On suede, many times you can use a soft suede brush or suede sponge and brush the water spot to remove the stain.
If that doesn't work, putting a layer of corn starch on the stain and letting it sit for a day or 2 (longer for especially bad stains) should solve the problem....vaccuum the corn starch off. It will not leave any residue on the coat.
Major stains should be treated by a dry cleaner, and ask if they are experienced with lambskin suede or shearling (depending on the type of coat you have). A specialist may have to treat the coat if the stain is very large or has been there a long time.
Once you have removed the stain, treat your garment with a non-silicone based water and stain repellent designed specifically for suede to prevent future issues. There are several brands out there, including one made by Totes.
Please let me know if I can help further in any way.