Lakes and ponds can be hotspots for CO2 and CH4 emissions, but Arctic studies remain scarce. Here we present diffusive and ebullition fluxes collected over several years from 30 ponds and 4 lakes formed on an organic‐rich polygonal tundra landscape. Water body morphology strongly affects the mixing regime—and thus the seasonal patterns in gas emissions—with ice‐out and autumnal turnover periods identified as hot moments in most cases. The studied thermokarst lake maintained relatively high ebullition rates of millennia‐old CH4 (up to 3405 14C YBP). Larger and deeper kettle lakes maintained low fluxes of both gases (century to millennium‐old), slowly turning into a CO2 sink over the summer. During winter, lakes accumulated CO2, which was emitted during the ice‐out period. Coalescent polygonal ponds, influenced by photosynthesizing benthic mats, were continuous CO2 sinks, yet important CH4 emitters (modern carbon). The highest fluxes were recorded from ice‐wedge trough ponds (up to 96 mmol CO2 equivalent m−2 d−1). However, despite clear signs of permafrost carbon inputs via active shore erosion, these sheltered ponds emitted modern to century‐old greenhouse gases. As the ice‐free period lengthens, scenarios of warmer and wetter conditions could favor both the production of CO2 and CH4 from thawing permafrost carbon, and CH4 production from recently fixed carbon through an atmospheric CO2‐to‐CH4 shunt at sites in which primary production is stimulated. This must be carefully considered at the landscape scale, recognizing that older carbon stocks can be mineralized efficiently in specific locations, such as in thermokarst lakes.