Matrix diffusion can be an effective contaminant retardation process in the geological environment surrounding a repository (e.g. geological disposal of high level radioactive waste (HLW)). However, long-term processes of matrix diffusion and redox front formation along fractures in sedimentary rocks have received relatively little attention. Here, we describe processes of element migration, enhanced by a biogenic redox reaction, along a groundwater-conducting fracture over the last ca 10 5 years in a Tertiary tuffaceous sedimentary sequence in Japan. The redox front identified along a single tension fracture is characterized by Fe oxide and by the concentration of some major and trace elements. Detailed geochemical analysis, EPMA and SEM–EDS examination, and microbial studies have been carried out to understand the processes of matrix diffusion, as well as the effect of microbial activity on redox front formation in sedimentary rock. The results show that ferric iron has been concentrated in the rock matrices even though there is little oxidant. Detailed SEM observation revealed iron-silica pellets encrusted with microbial colonies (presumably iron-oxidizing bacteria) in the micro porosity of the matrix. In places, microbial mats with bacterial cells were also identified. SEM–EDS analysis of the microbial mats showed that they include amorphous granules made exclusively of Fe and Si. Total cell counts in the order of 10 6 cells g − 1 were also carried out in the Fe oxide concentration zone by direct counting using a fluorescent dye. Incubation experiments under a reducing atmosphere suggest that a type of iron oxide microbe is still actively forming microscopic spherical iron particles and ferric iron at the front. These findings suggest that microbial activity can contribute to both redox front formation and substantial elemental migration from the fracture surface into the rock matrix. The observations made here have implications for understanding the long-term process of matrix diffusion along the sedimentary fractures that can be expected in the neighbourhood of HLW disposal sites.