Numerous field, laboratory, and modeling studies have explored the flows of fluid, heat, and solutes during seafloor hydrothermal circulation, but it has been challenging to determine transport rates and flow directions within natural systems. Here we present results from the first cross-hole tracer experiment in the upper oceanic crust, using four subseafloor borehole observatories equipped with autonomous samplers to track the transport of a dissolved tracer (sulfur hexafluoride, SF6) injected into a ridge-flank hydrothermal system. During the first three years after tracer injection, SF6 was transported both north and south through the basaltic aquifer. The observed tracer transport rate of ∼2–3 m/day is orders of magnitude greater than bulk rates of flow inferred from thermal and chemical observations and calculated with coupled fluid-heat flow simulations. Taken together, these results suggest that the effective porosity of the upper volcanic crust through which much tracer was transported is <1%, with fluid flowing rapidly along a few well-connected channels. This is consistent with the heterogeneous (layered, faulted, and/or fractured) nature of the volcanic upper oceanic crust.