To enable safe geological storage of high-level radioactive waste, a comprehensive understanding of the overall system must include relevant physical processes, geological and geotechnical boundary conditions. In the Mont Terri Rock Laboratory (Switzerland) the Cyclic Deformation (CD-A) experiment has been established with the excavation of the two twin niches in the year 2019. To study the impact of the different climatic conditions on the hydraulic and mechanical processes in the claystone, an extensive investigation program has been carried out. As part of the CD-A experiment, we present here a multidisciplinary interpretation including geological characterisation, geodetic and geotechnical measurements, numerical modelling and visualisation techniques. The period under consideration runs between September 2019 and March 2021. Geological mappings illustrate different zones of tectonically induced faulted rock in the sandy facies of the Opalinus Clay and laserscans conducted at regular intervals show small convergence of the niches. While the deformation around the open niche tends to continue, extensometer measurements around the closed twin indicate a reduced deformation after the first months. First coupled hydraulic–mechanical simulations demonstrate that the numerical approach is capable of reproducing the hydro-mechanical behaviour qualitatively, including the extent of the desaturated zone. The application of state-of-the-art visualisation techniques allows simultaneous evaluation and comparison of geological features, measurements and simulation results. This holistic approach – discussed here exemplary for the mechanical effects – provides a valuable basis for the rating of the impact of geologic structures, material heterogeneities, and climatic conditions on the Opalinus Clay. Thus, it can be a valuable component for the safe construction and operation of a repository and for the long term safety assessment.