Flow modelling using alternative assumptions regarding conceptual and parametric uncertainty in the spatial and structural relationships among fractures indicates elevated flow rates and groundwater velocities to deposition holes compared to SKB’s flow modelling results. Simulated sampling of fractures in boreholes does not indicate any reason to exclude the proposed spatial and structural relationships among fractures. The number of deposition holes that need to be discarded due to intersections with fractures, according to rules proposed by SKB, are not significantly affected by the studied alternative assumptions. Simulated fracture sampling along tunnels in the proposed repository layout for the Forsmark site indicates that future underground data should be sufficient to distinguish between SKB’s assumptions and the alternative ones made in this work. Whether or not the differences between different assumed spatial and structural relationships are robust with respect to non-ideal sampling situations underground is an open question.