<p>SUPPLEMENTARY MATERIAL FOR ONLINE PUBLICATION ONLY</p><p>Appendix 1</p><p>Calculation of the upper mixed layer depth</p><p>We determined the physical separation between the two layers by computing daily values of the upper mixed layer depth (Zmix). The upper mixed layer is considered relatively vertically homogenous in temperature, density and gas. As the thermocline is defined as the depth of the maximum change in temperature, we defined Zmix as the maximum change in temperature changes, which is computed as the maximum second derivative of temperature profile. Because temperature measurements are taken at discrete depth intervals, precise mixed layer depths are difficult to acquire. To resolve this issue without having to linearly interpolate between measurements, a temperature profile curve was fit by minimizing the sum of squares to a temperature curve model (Minns and Shuter 2012) before computing Zmix. The following figure shows an example of temperature profiles in</p><p>Lake Croche (upper panel) and Lake Simoncouche (lower panel), then the temperature change (first derivative) with the peak representing the thermocline (gray dot line) and a typical definition of the upper mixed layer (0.5C m-1, gray dash line), then the change in temperature change (second derivative) showing 2 peaks. The first one is the upper mixed layer (black dash line). The upper mixed layer depth corresponded remarkably well with the depth at which CO2 starts to accumulate (last graph to the right). Appendix 2</p><p>Soil pore water p CO2 measurements</p><p>Point measurements of soil pore-water pCO2 were taken monthly in both watersheds, at 3 different locations. Piezometers made of plastic tubes (inner diameter of 2.54cm) were placed in the soil at approximately 3-5 meters from the lake shore, to collect soil pore water at about 20 to 30 cm deep, depending on site soil thickness. Piezometers were flushed 24 hours prior to sampling, to discard stagnant waters. When the piezometer is replenished (approx. 24 h after flushing), we gently pumped the water out of the piezometer using a peristaltic pump 10ml into 60ml syringes (3 times) to create a 1:5 air- water ratio, with ambient air of known CO2 concentration. Syringes were then vigorously shaken for 1min to have a complete equilibrium. Headspaces were injected in an IRGA</p><p>(EGM-4, PPsystems) and pCO2 of water was back-calculated. The following figure shows the average soil pore water pCO2 of the sampled months during the study period in both lakes. References</p><p>Minns C and Shuter B. 2012. A semi-mechanistic seasonal temperature-profile model (STM) for the period of stratification in dimictic lakes. Canadian Journal of Fisheries and Aquatic Sciences. 181:169–181.</p>