A granite block, acquired from a quarry Panská Dubenka located in the Czech Republic and used in presented experiments, is part of the same bedrock that can be potentially used for a deep geological repository. It is important to characterize advection in fractured rock to assess possible groundwater contamination. Newly used method—three-dimensional scanning using Hexagon Romer Arm was implemented to characterize the morphology of an examined fractured block with a aperture. The scanning technology provides the possibility to digitalize the rock surface. The scanning can be also used to determine any changes in the rock surface. The block was instrumented by tubing, and the aperture was sealed using a silicone. Flow paths were investigated by the comparison of fluid weights on the outlet on every output/site. The Hexagon Romer Arm is an ideal tool for the precise determination of a aperture's width in its full volume.

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