The paper presents examples of work on groundwater flow and solute transport using the multidimensional model combining discrete fractures with continuum, within the Czech program of the deep geological repository implementation. The improvements in the numerical methods are described and the implementation within the open-source software Flow123d is introduced. The first model problem is a hydraulic and transport evaluation of a repository candidate site. The hydraulic model comprises depth variability of permeability, lithological groups, and tectonic planes represented by discrete features in the model. The model is calibrated on the borehole water levels, discharge balance, and water ages. Travel time from the repository to the ground is then evaluated. The second problem is a hydraulic and stress effect of excavation, which is the first step in the evaluation of hydraulic test relevance for the real rock properties. Models with homogeneous rock, matrix with stochastic discrete fractures, and both stochastic and deterministic fractures are compared. The effect of fractures on the flow is dominant for the third variant.

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