Abstract The spatial distribution of porosity and permeability of the Rupel Clay Member is of key importance to evaluate the spatial variation of its sealing capacity and groundwater flow condition. There are only a limited number of measured porosity and permeability data of the Rupel Clay Member in the onshore Netherlands and these data are restricted to shallow depths in the order of tens of metres below surface. Grain sizes measured by laser diffraction and SediGraph® in samples of the Rupel Clay Member taken from boreholes spread across the country were used to generate new porosity and permeability data for the Rupel Clay Member located at greater burial depth. Effective stress and clay content are important parameters in the applied grain-size based calculations of porosity and permeability. The calculation method was first tested on measured data of the Belgian Boom Clay. The test results showed good agreement between calculated permeability and measured hydraulic conductivity for depths exceeding 200m. The spatial variation in lithology, heterogeneity and also burial depth of the Rupel Clay Member in the Netherlands are apparent in the variation of the calculated permeability. The samples from the north of the country consist almost entirely of muds and as a consequence show little lithology-related variation in permeability. The vertical variation in permeability in the more heterogeneous Rupel Clay Member in the southern and east-southeastern part of the country can reach several orders of magnitude due to increased permeability of the coarser-grained layers.