Coalbed gas content and composition are critical for the successful exploration and production of coalbed methane. We investigated the differential transport of a preadsorbed CO2-CH4 gas mixture along a coalbed aquifer by groundwater flow or across a coal bed by upward diffusion through pore water. Consistent analytical approximations and numerical solutions were obtained for typical cases. The results suggest that differential transport of CH4 and CO2 in a water-saturated coal seam is mainly controlled by their adsorption equilibrium in coals and solubilities in water. Although CO2 is about 20 times more soluble than CH4 in water at temperatures lower than 50°C, the transport of CO2 from a coal seam is only several times more efficient than that of CH4 because of the stronger adsorption of CO2 than CH4 in coals. Preferential transport of CO2 over CH4 by groundwater advection can substantially accumulate more gas rich in CO2 at downstream or near discharge zones if gas-trapping structures exist, and it may cause low total gas content of CH4 near recharge zones, which may explain the CO2 and CH4 distribution in the San Juan and Powder River basins and the undersaturation of gas in many other coals. The separation and redistribution of coalbed gas by transport processes may also be complicated by late-stage biogenic gas generation with infiltration of meteoric water with nutrients and gas-producing microbes into the coal beds as suggested for some basins. Overall, hydrogeologic systems strongly influence the distribution of coalbed gas content and composition in coal seams.