Reducing the water crossover from anode to cathode is an important goal for direct methanol fuel cell (DMFC) technology, especially if highly concentrated methanol fuel is to be used. A well-documented way to reduce this water loss to the cathode side is by using a hydrophobic cathode microporous layer (MPL). Recently, however, it has been demonstrated that in addition to a cathode MPL, the use of a hydrophobic anode MPL further reduces the water loss to the cathode. In this work, we use a two-phase transport model that accounts for capillary induced liquid flow in porous media to explain physically how a hydrophobic anode MPL acts to control the net water transport from anode to cathode. Additionally, we perform a case study and show that a thicker, more hydrophobic anode MPL with lower permeability is most effective in controlling the net water transport from anode to cathode.