Anthropogenic nitrogen (N) inputs have been found to influence emissions of greenhouse gases from a variety of ecosystems; however, the effects of N loading on greenhouse gas dynamics in lakes are not well documented. We measured concentrations of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in 26 lakes in the Colorado Rocky Mountains (USA) receiving elevated (5 – 8 kg N ha−1 yr−1) or low (<2 kg N ha−1 y−1) levels of atmospheric N deposition. The mean CO2 concentration in surface waters was 27 μmol L−1 and did not differ between deposition regions. The CH4 concentration was greater in low-deposition lakes (167 nmol L−1) compared to high-deposition lakes (48 nmol L−1), while the opposite was true for N2O. The concentration of N2O in surface water averaged 29 nmol L−1 in high-deposition lakes compared to 22 nmol L−1 in low-deposition lakes. Nitrous oxide is of particular interest because it is more potent than CO2 as a greenhouse gas and because of its role in the destruction of stratospheric ozone. To understand the potential magnitude of lake N2O production related to atmospheric N deposition, we applied two published methodologies for determining emissions from aquatic ecosystems to available data sets. We estimated contemporary global N2O emissions from lakes to be 0.04 – 2 Tg N y−1, increasing to 0.1 – 3.4 Tg N y−1 in 2050. The contemporary estimates represent 13–95% of emissions from rivers and estuaries, suggesting that further research is required to better quantify emission rates from lentic ecosystems.