Abstract: A method and apparatus for actively monitoring conditions of a plasma source for adjustment and control of the source and to detect the presence of unwanted contaminant species in a plasma reaction chamber. Preferred embodiments include a spectrometer used to quantify components of the plasma. A system controller is provided that uses feedback loops based on spectral analysis of the plasma to regulate the ion composition of the plasma source. The system also provides endpointing means based on spectral analysis to determine when cleaning of the plasma source is completed.