The plasma parameters and relative positive and negative ion concentrations in a small, filtered, multicusp ion source, operating at low plasma density (<1*1011 cm-3) with both hydrogen and deuterium gas have been measured using a Langmuir probe and a small mass spectrometer. Under identical source operating conditions the plasma density in D2 is found always to be higher than in H2, while the negative ion density is found to be consistently lower in D2 then in H2. The effect of the different isotopes on transport processes in the discharge can be understood in terms of a simple model. The isotope effect on molecular processes is also discussed.