The good physical and chemical properties of CFRPEEK make it advantageous as a friction pair for water hydraulic components. This paper investigated the effects of surface topography and wettability on the tribological properties of CFRPEEK and 316 L under water lubrication, with emphasis on four topographies of hemispherical pit, conical pit, ellipsoidal pit and wedge-shaped pit. From the experimental results, the ellipsoidal pit CFRPEEK samples exhibited the best tribological properties and better wettability. An interesting phenomenon was found that when the contact angle of the CFRPEEK sample is small, the friction coefficient and the wear scar depth are also small. In conclusion, taking the ellipsoidal pit as the surface topography of the CFRPEEK sample is conducive to improving its wettability, and promote the formation of stable water film, thereby improving its performance, reducing wear and increasing its service life.