This paper presents petrographic, chemical, and isotopic (Sr, S) analyses of whole rock samples from a 1.8 km section of upper ocean crust (DSDP/ODP Hole 504B). The samples were selected to cover all lithologies (pillows, flows, breccias, dikes) and alteration/mineralization styles. The chemical and petrographic data were used to calculate weighted averages for upper crustal composition, based on which seawater-ocean crust exchange fluxes were calculated. These results confirm earlier estimates that identify the upper crust as a significant sink for K and Mg and a source of Ca and Si to the oceans. Changes in trace element geochemistry implies that the upper ocean crust in 504B is a sink for CO2, Rb, Cs, and U, although the flux rates are an order of magnitude smaller than suggests by previous estimates for DSDP Sites 417 and 418 in 118 Ma Atlantic crust. Fluxes of these components are similar, within a factor of four, to flux rates estimated for the Juan de Fuca Ridge flank, which may relate to similarities in the thermal and hydrogeological evolution at both sites that is controlled by rapid termination of fluid circulation and conductive reheating of the upper crust. The contrast between the fluxes of trace elements derived for those settings and the open-ocean sites 417/418 likely reflects prolonged fluid-rock interaction at the latter location. If the Mg uptake and Sr exchange reconstructed from 504B core is representative, ridge flank hydrothermal alteration cannot account for the imbalance in the Mg and Sr budgets of the oceans. Up to 10% of the crustal Pb resides in the mineralized parts of the transition zone between the volcanic section and the sheeted dike complex. Combined, the Pb mobilized in the deepest parts of the hydrothermal systems (probably not penetrated in 504B) and hosted in metalliferous sediments and mineralized stockwork may account for the Pb surplus of the continental crust and the evolution of Ce/Pb of the mantle. Hydrothermal alteration results in net increases of Rb/Sr and U/Pb, in particular in the uppermost 600 m of crust, but the increases are not large enough to make altered upper ocean crust a plausible precursor for the HIMU mantle component. Moreover, the fractionation between Th and Pb, if any, is insufficient to account for the development of highly radiogenic 208Pb/204Pb in a HIMU mantle source. Potential HIMU precursors can be derived from altered ocean crust after 1–2 Ga, if on the order of 80–90% Pb, 40–55% Rb, 40% Sr, and 35–40%U are removed during partial dehydration in subduction zones.