Since the first systematic mapping of the East Pacific Rise, its axial depth profile has been used to infer variability in magma supply or mantle temperature. Here, however, we show that segment-scale, rise-parallel undulations of both on- and off-axis seafloor depth result primarily from variations in the bulk density of oceanic crust. Using seismic images of crustal and upper mantle structure combined with gravity data and lava chemistry, we demonstrate that segment-scale variations in crustal density are caused by magmatic differentiation. Rise-parallel changes in magmatic differentiation are attributed to a skew between the axes of mantle upwelling and plate spreading. We conclude that segmentation of axial depth along fast-spreading ridges is controlled primarily by the geometry of mantle upwelling.