A large fraction of radioactive beams produced and delivered at TRIUMF’s isotope separator and accelerator facility, ISAC, are using either a surface ion source or a resonant ionization laser ion source, which share a common design. To characterize the operation of the ion sources, simulations were performed to determine the ion beam optics and beam envelope properties of the extracted beam. Furthermore ion-optics calculations were performed to determine the transmission parameters through the mass separator magnet. Emittances are measured in the ISAC low energy beam line right after the mass separator. The recent addition of a channeltron to the Allison emittance meter scanner now allows us to measure emittances for ion beams with intensities as low as 105ions/s. This is particularly useful for establishing high resolution, high throughput mass separator tunes for radioactive isotope beams. This paper discusses emittance measurements of low intensity beams, typical emittance scans for the surface ion source and the resonant laser ionized source for different source parameters. The observed results are compared to the simulations and discussed.