It is important to understand the long-term migration of radionuclides when considering long-lasting rock engineering projects such as the geological disposal of radioactive waste. The network of fractures and pores in a rock mass plays a major role in fluid migration as it provides pathways for fluid flow. The geometry of such a network can change due to fracture sealing by fine-grained material over extended periods of time. Groundwater commonly contains fine-grained material such as clay minerals, and it is probable that such minerals accumulate within rock fractures during groundwater flow, thereby decreasing fracture apertures and bulk permeability. It is therefore essential to conduct permeability measurements using water that includes fine-grained minerals in order to understand the evolving permeability characteristics of rock. However, this has not been studied to date in in-situ rock mass. Therefore, in the present study, we perform permeability measurements in a granite rock mass to investigate the change of permeability that occurs under the flow of water that includes clays. Our findings show that clay particles accumulate in fractures and that the permeability (hydraulic conductivity) of the granite rock mass decreases over time. The decrease was more significant in the earlier time. We conclude that the accumulation of clay minerals in the fracture decreases the permeability of a rock mass. Furthermore, we consider that the filling and closure of fractures in rock is possible under the flow of groundwater that contains clay minerals.