Increasing the efficiency of passive fuel cells is a significant hurdle in commercializing small fuel cells. By understanding the interactions within a single cell, possibilities for further performance increases in fuel cell structures overall are uncovered. To investigate the multiphase flows and the interactions between the layers on the anode side of a direct methanol fuel cell (DMFC), a single cell was studied using a two-dimensional model. This multiphase model focuses on the flow mechanism of a single CO2 gas bubble. The model describes the mass transfer in a single cell by using the physical properties of a single bubble and by tracing its movement. The simulation results indicate that the thickness of a gas diffusion layer (GDL) has an effect on the CO2 bubble size at a low power output level. When the power output is increased, the porosity and the GDL’s contact angle with CO2 play a significant role in determining the size of the CO2 bubbles. The final bubble size and the time it takes for the bubbles to penetrate the layers of the DMFC are controlled by the physical properties of the GDL and by the power output. The model suggests that, to achieve optimal performance, the GDL in passive DMFCs should be thick enough to allow bubbles grow to their maximum size. The thickness of the GDL can be calculated by estimating the maximum size of the bubble.