Permeability is a primary control on fluid flow within mid-ocean ridge hydrothermal systems and strongly influences the transfer of energy and mass between the ocean and the lithosphere. Little is known about how this parameter might vary in zero-age crust even though such variations may determine the locations and areal extents of upflow and downflow zones. Typically, estimates of permeability in seafloor environments are given as a single value (or range of values) for entire systems. Here we model crustal stresses inferred from poroelastically triggered earthquake patterns to estimate the two-dimensional permeability structure within a hydrothermal system on the East Pacific Rise at 9°50′N. We show that permeability in young ocean crust may vary by several orders of magnitude over horizontal scales of hundreds of meters with values ranging from 10−13.4 to 10−9.4 m2. Such values are consistent with other estimates of permeability in ocean crust. These variations may prescribe the geometry of hydrothermal convection and should be considered in future models of these systems.