An on-line halogen analyzer system and method of use for semiconductor processing effluent monitoring. The system includes sampling the effluent stream into an absorption cell, and passing UV-Visible light through the effluent sample in the cell. After passing through the sample the light is collected by a photo detector for real-time wavelength-selective absorption analysis. The system provides simultaneous determination of the concentrations of multiple halogen gases (e.g. F2, Cl2, Br2, and I2) in semiconductor processing effluent streams. The invention can be used for chemical vapor deposition (CVD) chamber cleaning endpoint determination and to improve fluorine utilization efficiency in remote plasma downstream CVD chamber cleaning processes.