Inland waters are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Ponds have amongst the highest CO2 and CH4 fluxes of all aquatic ecosystems, yet seasonal variation in fluxes remain poorly characterized, creating challenges for accurately estimating annual emissions. Further, ponds can exhibit a range of mixing regimes, yet the impact of mixing regimes on gas emissions remains unclear. Here, we assessed annual dynamics of CO2 and CH4 in four temperate ponds (Minnesota, USA) that varied in mixing regimes. The ponds ranged from annual sinks to sources of CO2 (−1 to 15 mol m−2 yr−1) and were all significant sources of CH4 (4.3–8.2 mol m−2 yr−1), with annual fluxes in CO2 equivalents of 1.8–4.1 kg CO2-eq. m−2 yr−1. Mixing regimes impacted CO2 and CH4 dynamics, as stratified periods were associated with more anoxia, greater accumulation of gases in the bottom waters, higher emissions of CH4, and lower fluxes of CO2. Ponds with stronger summer stratification also had increased CO2 and CH4 fluxes associated with fall turnover. Overall, the two ponds with the strongest stratification had higher annual fluxes (2.6, 4.1 kg CO2-eq. m−2 yr−1) compared to the two ponds that more frequently mixed (1.8, 2.2 kg CO2-eq. m−2 yr−1).