The harvesting of salinity gradient energy through a capacitive double-layer expansion (CDLE) technique is directly associated with ion adsorption and desorption in electrodes. Herein, we show that energy extraction can be modulated by regulating ion adsorption/desorption through water flow. The flow effects on the output energy, capacitance, and energy density under practical conditions are systematically investigated from a theoretical perspective, upon which the optimal operating condition is identified for energy extraction. We demonstrate that the net charge accumulation displays a negative correlation with the water flow velocity and so does the surface charge density, and this causes a nontrivial variation in the magnitude of output energy when water flows are introduced. When high water flows are introduced in both the charging and discharging processes, the energy extraction can be significantly reduced by 47.69-49.32%. However, when a high flow is solely exerted in the discharging process, the energy extraction can be enhanced by 12.94-14.49% even at low operation voltages. This study not only offers a comprehensive understanding of the microscopic mechanisms of surface-engineered energy extraction with water flows but also provides a novel direction for energy extraction enhancement.