Classical active seismic methods fail to sharply image the earth's deep crust. We present the first crustal-scale application of 2-D full waveform inversion based on dense ocean bottom seismic data to investigate the Eastern Nankai subduction system (Japan). This approach allows to quantify seismic velocities up to an unprecedented degree of resolution. Results reveal compressive tectonic features within both the subducting oceanic crust and the backstop. At depth, velocity anomalies along major faults and structural discontinuities bring evidence for the presence of fluids and weakened material and also for a possible co-seismic slip partitioning structure.