Flow separation near the fluid–solid surface has attracted attention for decades. It is critical to understand the behavior of separated flow adjacent to the solid walls to broaden its range of potential applications. Therefore, we conducted molecular dynamics investigations to consider water flow separation at the water–carbon nanotube (CNT) interface for different diameters of CNTs between 13 and 50 Å and different pressures of 0.1–1.254 GPa. Density heat maps indicated that water flow separation is observed for all CNTs under high pressures, and an empty space of water molecules or evacuation is formed behind the CNTs. It is shown that in CNTs with small diameters, (10, 10) and (20, 20), the structure of the first layer (FL) of water molecules or hydrated layer adjacent to the CNT wall is completely preserved, indicating that evacuation occurs from behind the CNTs. In (30, 30) and (40, 40) CNTs, flow separation occurred from the FL of water molecules near the solid surface, and the layered structure of water around CNTs is completely destroyed. Our findings of fluid–solid and fluid–fluid interaction energies suggested that the flow separation can be due to an attraction between the FL of water molecules and CNT and a repulsion between the water molecules in the hydrated layer and the outer layers. Moreover, analyzing the relationship between the CNT size and flow separation revealed that in the case of small CNTs, there are extra water molecules that contribute to the structural stability of the hydrated layer by strengthening the repulsive interaction in the liquid–liquid surface.