Approximately 50% of the carbon (C) stored in forest ecosystems, on a global scale, is located in the boreal forest. Inundating boreal forest soil, for hydroelectric power production, changes soil organic matter decomposition and C transformation. Soil from three reservoirs, differing in their vegetative composition and soil organic C (SOC) stock, was collected at the Experimental Lakes Area, Canada, and incubated under drawdown and reflooded conditions. Soil organic C and soil total N concentrations (g kg−1) and soil δ13C and δ15N (‰) were significantly different (P < 0.05) between soil horizons within each reservoir. After 5 years of episodic flooding, there was a significantly greater SOC and N stock in the reservoirs compared with undisturbed soil. Flooding also resulted in a redistribution of SOC and N within the soil profile. CO2 and CH4 production rates were significantly greater when the soil was reflooded, and the highest CO2 and CH4 production rates came from the LFH horizons compared with a charred layer and the mineral soil. Although flooding led to the redistribution and a greater accumulation of SOC and N in the charred and mineral soil layers compared with undisturbed soil, the CO2 and CH4 production rates were lower from this part of the soil profile compared with the LFH layers. This suggested that the redistributed organic material was of lower quality compared with that of the LFH horizons.