Abstract Although the importance of gas-entry pressure in simulating two-phase liquid–gas flow in porous media has been studied at the column and borehole scales, its impact on the simulation of transient hydraulic-gas at different scales of a deep geological repository of radioactive waste (DGR) in low permeability clay rock during the post-closure phase has not yet been studied. The purpose of this work is to show that neglecting this phenomenon can lead to underestimation of the maximum gas pressure and water–gas fluxes simulated within the host rock and backfilled drift network. This could impact the performance of the engineered barrier system of a DGR. Simulations performed for a high-level waste disposal cell and for a simplified repository composed of hundreds of disposal cells situated in a clay host rock, show that gas preferentially migrates through the DGR components with low capillary entry pressures, such as the excavation damaged zone (Refers to the zone where fractures develop due to failure of the rock mass around galleries after tunneling) (EDZ), the engineered barriers materials (backfill, bentonite-plug…) and interfaces between the EDZ and these materials. Such a result could have significant consequences on the performance of a repository, due to the accumulation of gas in the drift network and high increase of gas pressure, which could lead to the host rock hydraulic fracturing.