This study performed the molecular dynamic simulations to investigate the boundary behavior of liquid water with entrapped gas bubbles over various hydrophilic roughened substrates. A “liquid–gas–vapor coexistence setup” was employed to maintain a constant thermodynamic state during individual equilibrium simulations and corresponding non-equilibrium Poiseuille flow cases. The two roughened substrates (Si(100) and graphite) adopted in this study present similar contact angles and slip length with gas-free fluid. By considering the effects of argon molecules at the interface, we demonstrated that the boundary slip behavior differed dramatically between these two rough wall channels. This divergence can be attributed to differences in the morphology of argon bubble at the interface due to discrepancies in the atomic arrangement and wall–fluid interaction energy. Furthermore, the density of gas at the interface had a significant impact on the effective slip length of the roughened graphite substrate, whereas shear rate \(\dot{\gamma }\) presented no noticeable influence. On the roughened Si(100) surface, the morphology of the argon bubbles exhibited far higher meniscus curvature and unstable properties under hydrodynamic effects. Thus, this substrate exhibited no slip to slight negative slip and no remarkable influence from either the density of gas at the interface or shear rate. In the present study, we demonstrate that the morphology and behavior of interfacial gas bubbles are influenced by the parameters of wall–fluid interaction as well as the atomic arrangement of the substrate. Our results related to nanochannel flow reveal that different surfaces, such as Si(100) and graphite, may possess similar intrinsic wettability; however, properties of the interfacial gas bubbles can lead to noticeable changes in interfacial characteristics resulting in various degrees of boundary slippage.