Scale production occurs during enhanced geothermal system (EGS) processes due to various conditions. The production of scales in pipes or fractured reservoir narrows the diameter of the injection and production well, decreasing permeability and reducing EGS efficiency. However, geothermal water flushing during EGS processes can be implemented to recover the permeability. In this study, an experimental instrument to simulate a geothermal system was applied to observe the chemical composition change of core and water samples. To simulate the EGS, an experiment was conducted by injecting the geothermal fluid in several cycles to the fractured core. Results showed that Si ions decreased in the geothermal fluid and permeability decreased due to precipitation. Thereafter, flushing was applied, and dissolution occurred inside the fracture, increasing the permeability.