We analyse 67 new conductive heat-flow measurements on the southern flank of the Costa Rica Rift (CRR). Heat-flow measurements cover five sites ranging in oceanic crustal age between approximately 1.6 and 5.7 Ma, and are co-located with a high-resolution multichannel seismic line that extends from slightly north of the first heat-flow site (1.6 Ma) to beyond ODP Hole 504B in 6.9 Ma crust. For the five heat-flow sites, the mean observed conductive heat flow is approximate to 85 mW m(-2). This value is approximately 30 per cent of the mean lithospheric heat flux expected from a half-space conductive cooling model, indicating that hydrothermal processes account for about 70 per cent of the heat loss. The advective heat loss fraction varies from site to site and is explained by a combination of outcrop to outcrop circulation through exposed basement outcrops and discharge through faults. Supercritical convection in Layer 2A extrusives occurs between 1.6 and 3.5 Ma, and flow through a thinly sedimented basement high occurs at 4.6 Ma. Advective heat loss diminishes rapidly between approximate to 4.5 and approximate to 5.7 Ma, which contrasts with plate cooling reference models that predict a significant deficit in conductive heat flow up to ages approximate to 65 +/- 10 Ma. At approximate to 5.7 Ma the CRR topography is buried under sediment with an average thickness of approximate to 150 m, and hydrothermal circulation in the basement becomes subcritical or perhaps marginally critical. The absence of significant advective heat loss at approximate to 5.7 Ma at the CRR is thus a function of both burial of basement exposure under the sediment load and a reduction in basement permeability that possibly occurs as a result of mineral precipitation and original permeability at the time of formation. Permeability is a non-monotonic function of age along the southern flank of the CRR, in general agreement with seismic velocity tomography interpretations that reflect variations in the degree of ridge-axis magma supply and tectonic extension. Hydrothermal circulation in the young oceanic crust at the southern flank of CRR is affected by the interplay and complex interconnectedness of variations in permeability, sediment thickness, topographical structure, and tectonic and magmatic activities with age.