The effects of hydrogen on the structure of Zr-based bulk metallic glasses were investigated by positron annihilation lifetime spectroscopy. Three lifetime components are identified, indicating the presence of three distinct size ranges for open volume defects in the glass. The concentration of the smallest sites identified as tetrahedral interstitial holes in the densely packed and the intermediate sites identified as flow defects, changes with hydrogen addition. The concentration of tetrahedral interstitial holes in Zr55Cu30Ni5Al10 alloys initially increases with the increase of hydrogen content. When Zr55Cu30Ni5Al10 alloys were prepared in Ar + 10%H-2 atmospheres, the concentration of tetrahedral interstitial holes reaches a maximum, which may provide a more dense random-packed structure. For Zr57Al10Cu15.4Ni12.6Nb5 alloys, the increase of hydrogen content causes a decrease in the concentration of tetrahedral interstitial holes and an increase in the concentration of flow defects.