In low-permeability systems, groundwater may be accompanied by separate-phase fluids, and measured pore water pressures may deviate from those expected in steady-state, single-phase systems. These same systems may be of interest for storage of nuclear waste in Deep Geologic Repositories. Therefore, it is important to understand the relationship between the presence of a separate phase and anomalous pressure development. At the Bruce site in Southern Ontario, a significant underpressure was observed, and there is evidence for the presence of gas-phase methane in situ. This study used a one-dimensional (vertical) numerical model of the subsurface down to a depth of 844 m beneath the Bruce site to evaluate possible effects of hydromechanical coupling with multiphase flow on pressure evolution during glacial loading and unloading. The simulated pressure conditions were affected strongly by the amount of methane initially present in the system, and the maximum simulated underpressure varied nonmonotonically with increasing initial methane content. When the initial methane content was below the solubility limit, exsolution led to underpressures that briefly exceeded those that formed in the single-phase case. At intermediate initial methane contents (sufficient to produce an immobile gas phase), the gas phase dampened the hydromechanical effects of the glacial cycle. At large initial methane contents (when a mobile gas phase was present), gas migration caused a large decrease in relative liquid permeability, which further contributed to underpressure development in the pore water. Multiple scenarios that spanned a range of initial methane contents yielded underpressures like those observed at the Bruce site.