An apparatus for thermally separating mercury and organic contaminants from inert substrate materials (such as soil, sludges, sediments, drilling muds and cuttings), comprising an essentially air-tight processing chamber having a substrate inlet and a substrate outlet, said chamber having two or more troughs for processing of the substrate, a means for indirectly heating the chamber, a means for moving substrate through the two or more throughs of the chamber from the substrate inlet to the substrate outlet, and a vapour condensate handling system for removing and condensing vapours from the chamber for processing to remove and recover contaminants.