A novel low-cost method for the combined, real-time, and in situ determination of dissolved methane and carbon dioxide concentrations in freshwater ecosystems was designed and developed. This method is based on the continuous sampling of water from a freshwater ecosystem to a gas/liquid exchange membrane. Dissolved gas is transferred through the membrane to a continuous flow of high purity nitrogen, which is then measured by an off-axis integrated cavity output spectrometer (OA-ICOS). This method, called M-ICOS, was carefully tested in a laboratory and was subsequently applied to four lakes in Mexico and Alaska with contrasting climates, ecologies, and morphologies. The M-ICOS method allowed for the determination of dissolved methane and carbon dioxide concentrations with a frequency of 1 Hz and with a method detection limit of 2.76 x 10-10 mol L-1 for methane and 1.5 x 10-7 mol L-1 for carbon dioxide. These detection limits are below saturated concentrations with respect to the atmosphere and significantly lower than the minimum concentrations previously reported in lakes. The method is easily operable by a single person from a small boat, and the small size of the suction probe allows the determination of dissolved gases with a minimized impact on shallow freshwater ecosystems.