We analyzed 25,675 traveltime residuals from a three-dimensional seismic tomographic inversion to investigate crack-induced seismic anisotropy in the upper oceanic crust. The study covered two regions with contrasting levels of magmatic activity on the western limb of the 9°N overlapping spreading center on the East Pacific Rise. The level of anisotropy gradually decreases with depth in the magmatically and hydrothermally active ridge region. In contrast, we observed a highly variable anisotropic structure in the magmatically and hydrothermally less active tip region at the end of the dying ridge segment: a weakly anisotropic layer beneath strongly anisotropic extrusive volcanic rocks is likely to be the result of relatively shallow cracks closed by hydrothermal precipitation. Strongly anisotropic dikes with inferred narrow and water-saturated cracks provide important along-axis pathways for the circulation of hydrothermal fluids beneath the shallow cracks in the less magmatically active regions. Furthermore, a significant clockwise rotation (20°–30°) of fast directions occurs in both regions with increasing depth. Such a rotation provides evidence that the geometry of the underlying crack structure of the western limb is significantly different from that defined by the bathymetric ridge crest.