Molecular diffusion is a key transport process for noble gases in water. Such diffusive transport is often thought to cause a mass-dependent fractionation of noble gas isotopes that is inversely proportional to the square root of the ratio of their atomic mass, referred to as the square root relation. Previous studies, challenged the commonly held assumption that the square root relation adequately describes the behaviour of noble gas isotopes diffusing through water. However, the effect of diffusion on noble gas isotopes has only been determined experimentally for He, Ne and Ar to date, whereas the extent of fractionation of Kr and Xe has not been measured. In the present study the fractionation of Kr and Xe isotopes diffusing through water immobilised by adding agar was quantified through measuring the respective isotope ratio after diffusing through the immobilised water. No fractionation of Kr and Xe isotopes was observed, even using high-precision noble gas analytics. These results complement our current understanding on isotopic fractionation of noble gases diffusing through water. Therefore this complete data set builds a robust basis to describe molecular diffusion of noble gases in water in a physical sound manner which is fundamental to assess the physical aspects of gas dynamics in aquatic systems. •Kinetic gas theory is not suitable to predict isotopic fractionation of Kr and Xe diffusing through water.•Quantum–mechanical interactions might determine Kr and Xe isotope diffusion in water.•Kr and Xe data complete our current understanding of noble gas diffusion in aquatic systems.