We present here the first comprehensive assessment of the carbon (C) footprint associated with the creation of a boreal hydroelectric reservoir (Eastmain-1 in northern Québec, Canada). This is the result of a large-scale, interdisciplinary study that spanned over a 7-years period (2003–2009), where we quantified the major C gas (CO2 and CH4) sources and sinks of the terrestrial and aquatic components of the pre-flood landscape, and also for the reservoir following the impoundment in 2006. The pre-flood landscape was roughly neutral in terms of C, and the balance between pre- and post-flood C sources/sinks indicates that the reservoir was initially (first year post-flood in 2006) a large net source of CO2 (2270 mg C m−2 d−1) but a much smaller source of CH4 (0.2 mg C m−2 d−1). While net CO2 emissions declined steeply in subsequent years (down to 835 mg C m−2 d−1 in 2009), net CH4 emissions remained constant or increased slightly relative to pre-flood emissions. Our results also suggest that the reservoir will continue to emit carbon gas over the long-term at rates exceeding the carbon footprint of the pre-flood landscape, although the sources of C supporting these emissions have yet to be determined. Extrapolation of these empirical trends over the projected life span (100 years) of the reservoir yields integrated long-term net C emissions per energy generation well below the range of the natural-gas combined-cycle, which is considered the current industry standard.