Flooding boreal forest ecosystems for hydroelectric power generation may release substantial amounts of carbon (C) to the atmosphere, contributing to global warming. The objectives of this study were to evaluate CO₂ and CH₄ production rates using spring/fall (14 °C) and summer (21 °C) temperatures under non-flooded and flooded conditions. Incubation temperatures represented the mean annual air temperature in May and September (14 °C), and in July (21 °C). Greenhouse gas production rates were quantified using laboratory incubations of 2 contrasting soil types (Humo-Ferric Podzol [very dry, mineral] and a Histic Folisol [moist, organic]) collected at the Experimental Lakes Area in northwestern Ontario, Canada. The mean production rate of CO₂ and CH₄ in the headspace of the incubation jars was significantly influenced by temperature, flooding and soil type. Results showed that the mean CO₂ (65 [Podzol]; 43 [Folisol]) and CH₄ (0.06 [Podzol]; 0.06 [Folisol]) production rates (µg·g^-1·d^-1) were significantly higher (P < 0.05) at 21 °C and in flooded treatments from both soil types. The greatest CO₂ and CH₄ production rates (µg·^-1·d^-1) occurred from the Folisol (110 [CO₂]; 0.03 [CH₄]) and the L and FH horizons of the Podzol (250 [CO₂]; 0.05 [CH₄]). Q₁₀ values showed that decomposition of soil organic matter was more temperature dependent in non-flooded treatments, with values ranging from 1.57 to 5.03, than in flooded treatments (1.31 to 3.58). The greatest loss of soil organic carbon relative to the original C content (g·m^-2) occurred in the Ah horizon of the Podzol in non-flooded (0.01% [14 °C]; 0.02% [21°C]) and flooded (0.02% [14 °C]; 0.03% [21 °C]) treatments and at both temperatures. Information presented in this paper helps to evaluate how 2 contrasting soil types (Podzol and Folisol) responded to flooding and provided further insight into the dynamics of greenhouse gas (GHG) production rates as a result of hydroelectric reservoir creation. This will aid in future planning, construction, and management of hydroelectric reservoirs to help minimize GHG emissions and boreal forest disturbance.