The present invention pertains to methods and apparatus for removal of one or more solutes from a supercritical process solution. Solute additives and contaminants are removed from supercritical processing solutions via a contaminant removal system that is either part of the process vessel itself or is part of a local recirculation loop in fluid communication with the process vessel. This invention provides supercritical processing methods and apparatus for the removal of additives and contaminants during circulation so that depressurization and substrate removal can occur without contamination. The removal in some cases, for example cleaning residue, can be done continuously during a process to improve its efficiency. Removal mechanisms may include separation, destruction, conversion of the contaminant to acceptable species, or combinations thereof.