Understanding and predicting potential failure mechanisms during the excavation and open drift stages of geological repository construction are among the crucial aspects of performance evaluation and safety assessment of nuclear waste storage facilities. The development of the Excavation Damage Zone (EDZ) and the generation of shrinkage-induced cracks during operational phases are prominent examples of failure mechanisms that can compromise the integrity of the repository systems. This study presents an integrated framework for investigating shrinkage-induced cracking of Opalinus Clay in niches and tunnels. To achieve this, the hybrid Finite Discrete Element Method (FDEM) is employed. The methodology incorporates a two-way staggered hydro-mechanical coupling scheme, where solid phase analysis relies on 2D FDEM and fluid flow is modeled using the nonlinear Richards’ equation and solved via Finite Volume discretization. To account for the effects of EDZ, characterized by a pronounced increase in hydraulic conductivity, a numerical simulation of tunnel excavation is first carried out. The resulting failure pattern around underground openings is then abstracted through the definition of an altered hydraulic conductivity field. Comparison of the numerical results with field observations demonstrates the framework’s ability to capture a wide range of failure mechanisms inherent in various stages of underground repository construction in Opalinus Clay.