We have performed a 3-D seismic refraction tomography of a 48 × 48 km2 area surrounding ODP site 757, which is planned to host an International Ocean Network (ION) permanent seismological observatory, called the Ninetyeast Ridge Observatory (NERO). The study area is located in the southern part of the Ninetyeast Ridge, the trail left by the Kerguelen hotspot on the Indian plate. The GEOMAR Research Centre for Marine Geosciences and the Federal Institute for Geosciences and Natural Resources acquired 18 wide-angle profiles recorded by 23 ocean bottom hydrophones during cruise SO131 of R/V Sonne in spring 1998. We apply a first arrival traveltime tomography technique using regularized inversion to recover the 3-D velocity structure relative to a 1-D background model that was constructed from a priori information and averaged traveltime data. The final velocity model revealed the crustal structure down to approximately 8 km depth. Resolution tests showed that structures with approximately 6 km horizontal extent can reliably be resolved down to that depth. The survey imaged the extrusive layer of the upper crust of the Ninetyeast Ridge, which varies in thickness between 3 and 4 km. A high-velocity anomaly coinciding with a positive magnetic anomaly represents a volcanic centre from which crust in this area is thought to have formed. A pronounced low-velocity anomaly is located underneath a thick sedimentary cover in a bathymetric depression. However, poor ray coverage of the uppermost kilometre of the crust in this area resulted in smearing of the shallow structure to a larger depth. Tests explicitly including the shallow low-velocity layer confirmed the existence of the deeper structure. The heterogeneity of the upper crust as observed by our study will have consequences for the waveforms of earthquake signals to be recorded by the future seismic observatory.