Low temperature hydrothermal systems hosted in the volcanic oceanic crust are responsible for ∼20% of Earth’s global heat loss. Marine sediment ponds comprise an important type setting on young ridge flanks where hydrothermal circulation advectively extracts lithospheric heat, but the nature of coupled fluid-heat transport in these settings remains poorly understood. Here we present coupled (fluid-heat) numerical simulations of ocean crustal hydrogeology in and below North Pond, a sediment pond on ∼8 Ma seafloor of the North Atlantic Ocean. Two- and three-dimensional simulations show that advective transport beneath North Pond is complex and time varying, with multiple spatial and temporal scales, consistent with seafloor and borehole observations. A unidirectional, single-pass flow system is neither favored nor needed to match the spatial distribution of seafloor heat flux through North Pond sediments. When the permeability of the crustal aquifer is relatively high (10−10–10−9 m2), simulations can replicate much of the observed variability and suppression of seafloor heat flux and can explain basement overpressures and transient perturbations in pressure and temperature in the upper volcanic crust. Simulation results can also help explain heterogeneity in pore fluid chemistry and microbiology in the crust. Although driven by the same physical processes, the dynamics of hydrothermal circulation below North Pond are different from those seen on “discharge-dominated” ridge flanks, where the permeability and exposed area of isolated basement outcrops control the extent of regional heat extraction.