The enrichment of heavy hydrogen isotopes (deuterium, tritium) is required to fulfill their increasing application demands, e.g., in isotope related tracing, cancer therapy and nuclear reaction plants. However, their exceedingly low natural abundance and the close resemblance of physiochemical properties to protium render them extremely difficult to be separated. In this thesis, we investigate hydrogen isotope transport and separation via layered and two-dimensional materials. Three different theoretical challenges are undertaken in this work: (1) identification of the transported hydrogen species (proton H+ or protium H atom) inside interstitial space of layered materials (hexagonal boron nitride, molybdenum disulfide and graphite) and elucidation of their transport mechanism; (2) separation of hydron (proton H+, deuteron D+, and triton T+) isotopes through vacancy-free graphene and hexagonal boron nitride monolayers; (3) capture of the extremely rare light helium isotope (3He) with atomically thin two-dimensional materials. In the case of hydrogen transport, the essential challenges are investigation of its mechanism as well as the identification of transported particles. Regarding the case of hydron isotope separation, the essential questions are whether or not pristine graphene is permeable to the isotopes, and how quantum tunneling and topological Stone-Wales 55-77 defects affect their permeation and separation through graphene. In the last case, to capture the light helium isotope, quantum tunneling, which favors the lighter particles, is utilized to harvest 3He using graphdiyne monolayer. Our results provide novel theoretical insights into hydrogen particle transport inside the interstitial space of van der Waals materials; they uncover the mechanism of hydron isotope separation through 2D graphene and hexagonal boron nitride monolayers; and they predict the influence of pure quantum tunneling on the enrichment of 3He through graphdiyne membrane.