An open dynamic chamber for the continuous monitoring of diffusive and ebullitive fluxes of methane (CH4) in aquatic ecosystems was designed and developed. This method is based on a standard floating chamber in which a well-defined carrier gas flows. The concentration of CH4 is measured continuously at the outlet of the chamber, and the flux is determined from a mass balance equation. The method was carefully tested in a laboratory and was subsequently applied to two lakes, in Mexico, with contrasting trophic states. We show here that the method allows for the continuous quantification of CH4 diffusive flux higher than 25 × 10–6 g m–2 h–1, the determination of ebullitive flux, and the individual characterization of bubbles larger than 1.50–1.72 mm in diameter. The method was also applied to determine carbon dioxide emissions (CO2). In that case, the method was less sensitive but allowed for the characterization of diffusive fluxes higher than 10 mg CO2 m–2 h–1 and of bubbles larger than 5.3–8.4 mm in diameter. This high-throughput method can be adapted to any gas detector at low cost, making it a convenient tool to better constrain greenhouse gas emission from freshwater ecosystems.