The aim of the present study was to evaluate the effect of water flow rate on the morphological features of dentin and shear bond strength (SBS) of self-etching resin cement after Er,Cr:YSGG laser etching. Dentin specimens obtained from extracted human third molars were randomly assigned to four groups (n = 23), including one that received no laser irradiation (control-group D) and three others with different laser parameters: 2.25 W, 50 Hz, 60% air with water flow rates of 19 mL/min-100% water (group A), 2.25 W, 50 Hz, 6.75 mL/min-50% water (group B), and 2.25 W, and 50 Hz, 2.75 mL/min-25% water (group C). The morphological features of each group were examined with scanning electron microscopy and atomic force microscopy. The SBS of resin cement disks (Panavia F2.0, Kuraray; Tokyo, Japan) (3 mm in diameter and 2 mm in height) to the dentin specimens was measured using a universal testing machine at a cross head speed of 0.5 mm/min. Bond strength values were analyzed with one-way ANOVA/Tukey tests. There were no significant differences between the SBS values of groups A and B (p > 0.05). However, the SBS values of these groups were significantly higher when compared to groups C and D (p < 0.001). Er,Cr:YSGG laser application with water flow rates of 6.75 or 19 mL/min resulted in better dentin surface alterations and increased the SBS of self-etching resin cement to dentin.