A commercially available electron cyclotron resonance (ECR) plasma source (GenII Plasma Source, tectra GmbH) is widely used for surface processing. This plasma source is compatible with ultrahigh vacuum systems, and its working pressure is relatively low, around 10−6–10−4 Torr even without differential pumping. Here, we report ion flux concentration ratios for each ion species in an ion beam from this source, as measured by a mass/energy analyzer that is a combination of a quadrupole mass spectrometer, an electrostatic energy analyzer, and focusing ion optics. The examined beams were those arising from plasmas produced from feed gases of H2, D2, N2, O2, Ar, and dry air over a range of input power and working pressures. H2(D2) plasmas are widely used for nuclear fusion applications and, hence, the ion concentration ratios of H+, H2+, and H3+ reported here will be useful information for research that applies this plasma source to well-controlled plasma-material interaction studies. Ion energy distributions, stability of operation, and impurity concentrations were also assessed for each of the plasma species investigated.