A water lubricating axial piston pump (WLPP) is the core power component of a green and environmentally friendly water hydraulic system. The friction and wear of the friction pairs of a WLPP are the key factors that restrict its development. In order to explore the friction and wear mechanism of materials, the tribological properties of CFRPEEK against 316L and 1Cr17Ni2 under water lubrication were investigated in a friction testing machine and an axial piston pump, respectively. An environmental scanning electron microscope (ESEM), confocal laser scanning microscopy and a surface profiler were used to analyze the morphology of the samples. In a friction testing machine, two different metals are paired with CFRPEEK, and the friction coefficient and wear rate barely show any differences. The wear rate of CFRPEEK is two orders of magnitude higher than that of metal. In the WLPP, 316L can hardly be paired with CFRPEEK, while 1Cr17Ni2 works well. The wear of 1Cr17Ni2 in the WLPP is greater than that of CFRPEEK. The high-pressure water film lubrication friction pairs cause the wear of the metal and show the difference in these two test methods. The wear mechanism is mainly abrasive wear. Improving the wear resistance of metals is very important for the development of WLPP.