Flooding land for water reservoir creation has many environmental impacts including the production of the greenhouse gases (GHG) carbon dioxide (CO2) and methane (CH4). To assess processes governing GHG emissions from the flooding of terrestrial carbon, three experimental reservoirs were constructed in upland boreal forest areas of differing carbon stores as part of the Flooded Upland Dynamics Experiment (FLUDEX). We calculated process-based GHG budgets for these reservoirs over 5 years following the onset of flooding. Stable isotopic budgets of carbon were necessary to separate community respiration (CR), which produces CO2, from net primary production (NPP), which consumes CO2, and to separate CH4 production from CH4 consumption via oxidation. NPP removed up to 44% of the CO2 produced from CR. CR and NPP exhibited different year-after-year trends. CH4 flux to the atmosphere increased about twofold over 3 years, yet isotopic budgets showed CH4 production in flooded soils increased nearly tenfold. CH4 oxidation near the flooded soil-water interface greatly decreased the CH4 flux from the water column to the atmosphere. Ebullition was the most important conduit of CH4 to the atmosphere after 3 years. Although CH4 production increased with time, the total GHG flux, in CO2 equivalents, declined. Contrary to expectations, neither CR nor total GHG fluxes were directly related to the quantity of organic carbon flooded. Instead, these reservoirs produced a strikingly similar amount of CO2 equivalents over 5 years.