Lakes and ponds cover only about 4% of the Earth’s non-glaciated surface1, yet they represent disproportionately large sources of methane and carbon dioxide2, 3, 4. Indeed, very small ponds (for example, <0.001 km2) may account for approximately 40% of all CH4 emissions from inland waters5. Understanding how greenhouse gas emissions from aquatic ecosystems will respond to global warming is therefore vital for forecasting biosphere–carbon cycle feedbacks. Here, we present findings on the long-term effects of warming on the fluxes of GHGs and rates of ecosystem metabolism in experimental ponds. We show that shifts in CH4 and CO2 fluxes, and rates of gross primary production and ecosystem respiration, observed in the first year became amplified over seven years of warming. The capacity to absorb CO2 was nearly halved after seven years of warmer conditions. The phenology of greenhouse gas fluxes was also altered, with CO2 drawdown and CH4 emissions peaking one month earlier in the warmed treatments. These findings show that warming can fundamentally alter the carbon balance of small ponds over a number of years, reducing their capacity to sequester CO2 and increasing emissions of CH4; such positive feedbacks could ultimately accelerate climate change.