The use of porous filters is indispensable in laboratory- and field-scale diffusion studies, where sample confinement is needed for mechanical reasons. Examples are diffusion studies with compacted swelling clays or brittle clay stones. Knowledge of the diffusion properties of these filters is important in cases where they contribute significantly to the overall diffusive resistance in the experimental setup. In the present study, measurements of effective diffusion coefficients (Db) in porous, stainless steel filter discs are reported for tritiated H2O (HTO), 22Na+, Cs+, and Sr2+ before and after use of the filters in diffusion experiments with different clay minerals. The Db values for used filters were found to be less than those of the as-received filters by ~30–50%. The Db values measured for the diffusion of HTO, 22Na+, Cs+, and Sr2+ in unused and used stainless steel filter discs correlated fairly well with the respective molecular diffusion coefficients in bulk water. Although such correlations are inherently associated with some uncertainties, they allow reasonable estimates to be made for diffusants for which no Db values are available. For the first time, a procedure is outlined that allows an integrative assessment to be made for the impact of the uncertainties in the filter diffusion properties on the combined standard uncertainties of the diffusion parameters obtained from through-diffusion experiments. This procedure can be used in the design and optimization of through-diffusion experiments in which the diffusive resistance of the porous filters must not be ignored. Shown here, as a general rule of thumb, is that, if the effective diffusion coefficient in the porous filter is at least three times larger than that in the clay, the choice of geometrical boundary conditions is rather uncritical, as long as the thickness of the clay sample is greater than that of the porous filters.