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Abstract We invertPg,PmP, andPntraveltimes from an active‐source, multiscale tomography experiment to constrain the three‐dimensional isotropic and anisotropicPwave velocity structure of the topmost oceanic mantle and crust and crustal thickness variations beneath the entire Endeavour segment of the Juan de Fuca Ridge. The isotropic velocity structure is characterized by a semicontinuous, narrow (5‐km‐wide) crustal low‐velocity volume that tracks the sinuous ridge axis. Across the Moho, the low‐velocity volume abruptly broadens to approximately 20 km in width and displays a north‐south linear trend that connects the two overlapping spreading centers bounding the segment. From the seismic results, we estimate the thermal structure and melt distribution beneath the Endeavour segment. The thermal structure indicates that the observed skew, or lateral offset, between the crustal and mantle magmatic systems is a consequence of differences in mechanisms of heat transfer at crustal and mantle depths, with the crust and mantle dominated by advection and conduction, respectively. Melt volume estimates exhibit significant along‐axis variations that coincide with the observed skew between the mantle and crustal magmatic systems, with sites of enhanced crustal melt volumes and vigorous hydrothermal activity corresponding to regions where the mantle and crustal magmatic systems are vertically aligned. These results contradict models of ridge segmentation that predict enhanced and reduced melt supply beneath the segment center and ends, respectively. Our results instead support a model in which segment‐scale skew between the crustal and mantle magmatic systems governs magmatic and hydrothermal processes at mid‐ocean ridges.