Abstract The Prototype Repository (PR) tunnel is located at the Äspö Hard Rock Laboratory near Oskarshamn in the southeast of Sweden. In the PR tunnel, six full-sized deposition holes (8.37 m deep and 1.75 m in diameter) have been constructed. Each deposition hole is designed to mimic the Swedish reference system for the disposal of nuclear fuel, KBS-3V. The PR experiment is designed to provide a full-scale simulation of the emplacement of heat-generating waste. There are three phases to the experiment: (1) the open tunnel phase following construction, where both the tunnel and deposition holes are open to atmospheric conditions; (2) the emplacement of canisters (containing heaters), backfill and seal in the first section of the tunnel; and (3) the emplacement of canisters, backfill and seal in the second section of the tunnel. This work describes the numerical modelling, performed as part of the engineered barrier systems (EBS) Task Force, to understand the thermo-hydraulic (TH) evolution of the PR experiment and to provide a better understanding of the interaction between the fractured rock and bentonite surrounding the canister at the scale of a single deposition tunnel. A coupled integrated TH model for predicting the wetting and the temperature of bentonite emplaced in fractured rock was developed, accounting for the heterogeneity of the fractured rock. In this model, geometrical uncertainties of fracture locations are modelled by using several stochastic realizations of the fracture network. The modelling methodology utilized information available at early stages of site characterization and included site statistics for fracture occurrence and properties, as well as proposed installation properties of the bentonite. The adopted approach provides an evaluation of the predictive capability of models, it gives an insight of the uncertainties to data and demonstrates that a simplified equivalent homogeneous description of the fractured host rock is insufficient to represent the bentonite resaturation.