We present three‐dimensional simulations of coupled fluid and heat transport in the ocean crust, to explore patterns and controls on ridge‐flank hydrothermal circulation on the eastern flank of the Juan de Fuca Ridge. Field studies have shown that there is large‐scale fluid flow in the volcanic ocean crust in this region, including local convection and circulation between two basement outcrops separated by ~50 km. New simulations include an assessment of crustal permeability and aquifer thickness, outcrop permeability, the potential influence of multiple discharging outcrops, and a comparison between two‐dimensional (profile) and three‐dimensional representations of the natural system. Field observations that help to constrain new simulations include a modest range of flow rates between recharging and discharging outcrops, secondary convection adjacent to the recharging outcrop, crustal permeability determinations made in boreholes, and the lack of a regional seafloor heat flux anomaly as a consequence of advective heat loss from the crust. Three‐dimensional simulations are most consistent with field observations when models use a crustal permeability of 3 × 10−13 to 2 × 10−12 m2, and the crustal aquifer is ≤300 m thick, values consistent with borehole observations. We find fluid flow rates and crustal cooling efficiencies that are an order of magnitude greater in three‐dimensional simulations than in two‐dimensional simulations using equivalent properties. Simulations including discharge from an additional outcrop can also replicate field observations but tend to increase the overall rate of recharge and reduce the flow rate at the primary discharge site.