Water management of membrane electrode assemblies (MEAs) has a significant impact on both the power performance and durability of anion exchange membrane fuel cells (AEMFCs). In this work, the hydrophobicity of catalyst layers (CLs) was systematically tuned using hydroxyl-functionalized and fluoroalkyl-functionalized carbon additives to improve water management. The inclusion of the fluorinated carbon in the anode CL effectively suppresses anode water flooding, whereas the hydroxyl-functionalized carbon additive in the cathode prevents cathode drying. The pairing of the hydrophobic anode CL and the hydrophilic cathode CL increases the maximum current density by 1.7 times compared with the carbon-additive-free MEA and ensures stable constant current operation for more than 1000 h due to the mitigation of water imbalance between the cathode and anode. This work highlights the importance of water management and provides simple and diversified means to tune the water distribution of an AEMFC.