A study has been made of the correlation between energetic positive plasma ions and the resulting Josephson tunnel barriers fabricated in an RF plasma. Typical edge junction current densities of 4000 Amp/cm2and Vm's of 25 mV were achieved. An in-situ mass spectrometer system was designed to extract, energy analyze, and identify the positive ion species incident on the RF cathode/sample surface. The argon positive ion measurements are correlated to Nb sputter rates and back scattered Pb and Nb rates - required for a clean Nb interface. The CH4positive ions are correlated to the growth of niobium carbide which reduces sub-oxide formation while optimizing junction quality. Finally the niobium oxide growth is correlated to the O2positive ion measurements. A simple model for oxide growth consisting of a time dependent O+2ion induced term and a time independent or very fast initial state term accounts for the known junction tunnel current dependencies on the RF plasma parameters of pressure, voltage, frequency, time, and ion to substrate angle.