A method for cleaning the fountain solution of a printing press with an automatically emptying separator (16), separates the dirt particles and oil residues from fountain solution and supplies them, as a mixture of dirt and fountain solution, to a dirt and fountain solution container (24) and passes the remaining fountain solution into a fountain solution storage tank (20). The dirt and fountain solution mixture in the dirt and fountain solution mixture container (24) is caused to settle in layers and the layer, containing the fountain solution, is transferred by an overflow (26) in to the fountain solution storage tank (20).