Hydrothermal circulation at mid-ocean ridges is responsible for ~25% of Earth’s heat flux and controls the thermal and chemical evolution of young oceanic crust. The heat flux of black smoker hydrothermal systems is thought to be primarily controlled by localized magma supply and crustal permeability. Nevertheless, magma chamber characteristics and the nature of crustal permeability beneath such systems remains unclear. Here we apply three-dimensional full-waveform inversion to seismic data from the hydrothermally active Endeavour segment of the Juan de Fuca Ridge to image the upper crust in high resolution. We resolve velocity variations directly above the axial magma chamber that correlate with variations in seismicity, black smoker heat flux, and the depth of the axial magmatic system. We conclude that localized magma recharge to the axial magma lens, along with induced seismogenic cracking and increased permeability, influences black smoker heat flux.