The plasma output of an electron cyclotron resonance source operating with hydrogen has been characterized using optical emission spectroscopy to observe neutral excited atomic hydrogen H* and a Langmuir probe to observe H+ as a function of currents to the two electromagnets producing the magnetic field. The rate at which the hydrogen plasma etches the surface oxide on InP substrates has been measured as a function of substrate temperature over the range 250–485 °C for two operating conditions, one that maximizes H* and the other for which a combination of high H+ and minimal H* occurs. The results indicate that the plasma stream with maximum H* etches approximately five times faster than the plasma stream with high H+ and low H* content. However, the activation energy of the etching reaction, Ea∼0.45 eV, is the same for the two plasma conditions. Considering the oxide as InPO4, produced by exposing the substrates to ozone generated by ultraviolet light, the proposed reaction for the etching is InPO4+7.3H→2H2O+0.5PH2 +0.5PH3+0.8InH+0.2In.