Very small ponds have been omitted from greenhouse gas budgets. Estimates of CO2 and CH4 emissions from 427 lakes and ponds show that very small ponds account for 15% of CO2 and 40% of diffusive CH4 emissions, but 8.6% of lake and pond area. Inland waters are an important component of the global carbon cycle. Although they contribute to greenhouse gas emissions1,2,3,4,5, estimates of carbon processing in these waters are uncertain. The global extent of very small ponds, with surface areas of less than 0.001 km2, is particularly difficult to map, resulting in their exclusion from greenhouse gas budget estimates. Here we combine estimates of the lake and pond global size distribution, gas exchange rates, and measurements of carbon dioxide and methane concentrations from 427 lakes and ponds ranging in surface area from 2.5 m2 to 674 km2. We estimate that non-running inland waters release 0.583 Pg C yr−1. Very small ponds comprise 8.6% of lakes and ponds by area globally, but account for 15.1% of CO2 emissions and 40.6% of diffusive CH4 emissions. In terms of CO2 equivalence, the ratio of CO2 to CH4 flux increases with surface area, from about 1.5 in very small ponds to about 19 in large lakes. The high fluxes from very small ponds probably result from shallow waters, high sediment and edge to water volume ratios, and frequent mixing. These attributes increase CO2 and CH4 supersaturation in the water and limit efficient methane oxidation. We conclude that very small ponds represent an important inland water carbon flux.