Fresh waters in general and ponds in particular are biogeochemical hot spots and as such are sources of greenhouse gas (GHG) emissions, especially methane (CH₄) and carbon dioxide (CO₂). Several studies have shown that thermal stratification of the water column is a common characteristic of ponds, but how this process influences GHG dynamics is less well studied. We tracked thermal stratification and the associated hypoxia in six ponds across the growing season and measured dissolved CH₄ and CO₂ in surface and bottom waters, along with CH₄ebullition, every two weeks. The results showed that all ponds stratified during the growing season and that thermal stratification often, but not always, led to bottom-water hypoxia. Where hypoxia occurred, bottom-water CH₄ was approximately 16 times higher (median 3.05 vs 0.19 mg C L^−1), CO₂ about 3 times higher (11.6 vs 4.03 mg C L^−1) and CH₄ ebullition was about 3.4 times higher than in oxic conditions. In contrast, surface-water GHG concentrations showed no significant difference between periods with and without bottom-water hypoxia. Bottom-water temperatures were not significantly different between hypoxic and oxic states, indicating oxygen availability, rather than temperature, dominated GHG buildup and ebullition. Stratification and the resulting hypoxia enhance CH₄ ebullition and promote high concentrations of GHGs in bottom waters, which may be released in small or larger pulses as the water column mixes partially or fully. In summary this study demonstrates that thermal stratification, by inducing bottom-water hypoxia, strongly influences the GHG dynamics across a range of timescales in ponds.