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Permeability controls energy and matter fluxes in deep‐sea hydrothermal systems fueling a 'deep biosphere' of microorganisms. Here, we indirectly measure changes in sub‐seafloor crustal permeability, based on the tidal response of high‐temperature hydrothermal vents at the East Pacific Rise 9°50’N preceding the last phase of volcanic eruptions during 2005–2006. Ten months before the last phase of the eruptions, permeability decreased, first rapidly, and then steadily as the stress built up, until hydrothermal flow stopped altogether ∼2 weeks prior to the January 2006 eruption phase. This trend was interrupted by abrupt permeability increases, attributable to dike injection during last phase of the eruptions, which released crustal stress, allowing hydrothermal flow to resume. These observations and models suggest that abrupt changes in crustal permeability caused by magmatic intrusion and volcanic eruption can control first‐order hydrothermal circulation processes. This methodology has the potential to aid eruption forecasting along the global mid‐ocean ridge network.