The Nankai Trough Seismogenic Zone Experiment (IODP), SW Japan, aimed at unraveling hydrologic processes at subduction megathrusts and in situ rock and fluid properties to understand the fault zone behavior during earthquake nucleation and rupture propagation. At different sites, characterization of the sediments at high resolution allows tracing fluid-rock reactions that are either associated to early transformations (hydration or dehydration of clay minerals) during the accretion phase or to mineral recrystallization processes linked to deformation phases in gouge zones. In the sedimentary strata at the front of the accretionary prism changes in clay composition are inferred from chemical trends observed in pore fluids, which further indicate the influence of volcanic ash alteration (zeolite formation). Along the megasplay fault, recrystallization processes (e.g. pyrite) are observed in foliated gouge zones at the contact with non-foliated silty clay. The data highlight the importance of small-scale observations for process and reactive phases such as clays in such variable fluid-sediment reactions.