Fractures are the predominant flow pathways in low-permeability rocks. Understanding the fluid-rock interactions that occur in rock fractures and their effects on fracture aperture variations is important for assessing the sustainability of reservoir productivity. This study presents two long-term flow-through experiments with fractured pure quartz sandstones to investigate how fluid composition affects fracture changes over time. One sample was continuously flowed through with fluids (DI or Si-rich fluid), while the other sample was subjected to intermittent flow (DI) at certain time intervals. The results show that the hydraulic aperture of the sample with intermittent flow maintains relatively constant, and the pore fluid is enriched with Si that is higher than the corresponding quartz solubility. On the contrary, hydraulic aperture reduces by 50% of its initial value in the case of continuous flow. The pore fluid Si concentrations are far below the quartz solubility. Based on the microstructure variations of contact asperities and the fluid concentration changes, we demonstrate that pressure solution plays a dominant role in rock fracture deformation and permeability changes. The pore fluid composition has a remarkable effect on the permeability decay process. The cumulative Si in the pore fluid without flow would mitigate fracture closure by limiting pressure solution. In contrast, the continuous injection of DI would lead to the continuous mass transfer between the contact asperities and the pore fluid. The permeability evolutions in the two cases are likely governed by the Si precipitation process and the stress-driving dissolution process, respectively.