We use coupled heat and mass transport models to investigate the basement permeability distribution and hydrothermal circulation patterns in an area with large basement relief below flat seafloor on the eastern flank of the Juan de Fuca Ridge. If heat transport around Ocean Drilling Program Sites 1026 and 1027 were purely conductive, the top of basement at Site 1027 (below ∼600 m of sediment) would be ∼50°C warmer than at Site 1026 (below ∼250 m of sediment), but the top of basement in this area is nearly isothermal. Vigorous fluid circulation in hydrothermal (uppermost) basement is required in order to maintain a near isothermal sediment-basement contact. We estimate the magnitude of hydrothermal basement permeability, test the reliability of conductive-proxy models used to estimate basement permeability for this setting, and examine the evolution of the hydrothermal circulation system as sediment accumulates. We find hydrothermal basement permeabilities ≥10−10 m2 are required for the top of basement near Sites 1026 and 1027 to be nearly isothermal, consistent with results from the conductive-proxy models. Modelled fluid circulation in the direction that allows both the observed sign of temperature difference between Sites 1026 and 1027 (warmer in the basement high) and a close approximation of the observed relative basement pressures is only achieved with a heterogeneous permeability distribution, connected high permeability conduits hosted within low permeability rock. This suggests that ridge flank hydrothermal circulation in this setting occurs dominantly within narrow zones of elevated permeability, consistent with observed, scale-dependent variations in permeability in this region, and conceptual models of heterogeneous hydrogeologic systems in general.