Lakes emit globally significant amounts of carbon dioxide (CO) to the atmosphere, but quantifying these rates for individual lakes is extremely challenging. The exchange of CO across the air-water interface is driven by physical, chemical, and biological processes in both the lake and the atmosphere that vary at multiple spatial and temporal scales. None of the methods we use to estimate CO flux fully capture this heterogeneous process. Here, we compared concurrent CO flux estimates from a single lake based on commonly used methods. These include floating chambers (FC), eddy covariance (EC), and two concentration gradient based methods labelled fixed (F-CO₂) and spatial (S-CO₂). At the end of summer, cumulative carbon fluxes were similar between EC, F-CO₂ and S-CO₂ methods (-4, -4 and -9.5 gC), while methods diverged in directionality of fluxes during the fall turnover period (-50, 43 and 38 gC). Collectively these results highlight the discrepancies among methods and the need to acknowledge the uncertainty when using any of them to approximate this heterogeneous process.