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Small freshwater reservoirs are ubiquitous and likely play an important role in global greenhouse gas (GHG) budgets relative to their limited water surface area. However, constraining annual GHG fluxes in small freshwater reservoirs is challenging given their footprint area and spatially and temporally variable emissions. To quantify the GHG budget of a small (0.1 km2) reservoir, we deployed an Eddy covariance (EC) system in a small reservoir located in southwestern Virginia, USA over 2 years to measure carbon dioxide (CO2) and methane (CH4) fluxes near-continuously. Fluxes were coupled with in situ sensors measuring multiple environmental parameters. Over both years, we found the reservoir to be a large source of CO2 (633–731 g CO2-C m−2 yr−1) and CH4 (1.02–1.29 g CH4-C m−2 yr−1) to the atmosphere, with substantial sub-daily, daily, weekly, and seasonal timescales of variability. For example, fluxes were substantially greater during the summer thermally stratified season as compared to the winter. In addition, we observed significantly greater GHG fluxes during winter intermittent ice-on conditions as compared to continuous ice-on conditions, suggesting GHG emissions from lakes and reservoirs may increase with predicted decreases in winter ice-cover. Finally, we identified several key environmental variables that may be driving reservoir GHG fluxes at multiple timescales, including, surface water temperature and thermocline depth followed by fluorescent dissolved organic matter. Overall, our novel year-round EC data from a small reservoir indicate that these freshwater ecosystems likely contribute a substantial amount of CO2 and CH4 to global GHG budgets, relative to their surface area.