Underwater laser ablation is typically used to scribe a silicon wafer with low thermal damage and less redeposition of cut debris on the workpiece surface. However, the hydrodynamic characteristics of water and some particles suspending in water are able to disturb the laser beam during the ablation. As such, the overall laser cutting performance in water and cut results can become poor or even unacceptable in some ablating conditions. This study thus aims at enhancing the underwater laser ablation process by controlling the water flow rate and flow direction in a closed water chamber setup. A single-crystalline silicon wafer selected as a work sample in this study was grooved by a nanosecond pulse laser under different water flow rates in order to carry the excessive heat and cut debris away from the workpiece. According to the experimental findings, a deeper groove and less redeposition can be obtained when the ablation was performed in a higher water flow rate. By processing silicon in the flowing water, the significant disturbances of air bubbles, water waves, and cut debris to the laser beam can be minimized, hence gaining a better ablating performance than the laser ablation in still water. Furthermore, the plastic deformation of silicon was evident as per the presence of slip bands on the cut surface, where the band size was found to decrease with the increased water flow rate.