A water spot remover cleared the minerals but I can still see the marks. What is happening?

The minerals are gone. What remains is etching that has bitten into the clear coat itself. Water-spot minerals are mildly acidic and, when left to bake in the sun, they eat into the clear coat and leave a permanent mark that no chemical product can lift. The only remedy at that stage is machine polishing, stepping up to compound if needed, or in severe cases wet sanding. Always tackle water spots early, starting with a pH-neutral wash and escalating to an acidic shampoo then a dedicated water-spot remover before considering correction.

Should I run a water spot remover before or after polishing?

Before polishing, not after. The bonded minerals and hard water deposits sitting on the clear coat are abrasive. If you polish over them, you drag those mineral particles across the paint and introduce fresh marring on top of the defects you were trying to remove. Removing them chemically first means your polish is only working the paint surface, not grinding mineral grit into it.

What can I use for light water marks after washing without reaching for a dedicated water spot remover?

Koch Chemie Fse (Finish Spray Exterior) is a quick detailer with a mild acid that tackles light water marks on paint and glass. Use it regularly after washing as a preventive step. For more established mineral deposits that Fse does not shift, step up to a dedicated acidic product such as CarPro DScale or Garage Therapy Descale.

Can a water spot remover or acidic shampoo revive a neglected ceramic coating?

Yes, often substantially. On a ceramic-coated car with heavy water spots and degraded hydrophobics, a water spot remover pass followed by a CarPro DScale acidic shampoo contact wash can remove the mineral and iron contamination that is masking the coating underneath and substantially revive the coating's water repellency without re-coating. Run the iron fallout remover first, then the water spot remover, to give the coating the cleanest base to work from.