Small waterbodies have potentially high greenhouse gas emissions relative to their small footprint on the landscape, although there is high uncertainty in model estimates. Scaling their carbon dioxide (CO₂) and methane (CH₄) exchange with the atmosphere remains challenging due to an incomplete understanding and characterization of spatial and temporal variability in CO₂ and CH₄. Here, we measured partial pressures of CO₂ (pCO₂) and CH₄ (pCH₄) across 30 ponds and shallow lakes during summer in temperate regions of Europe and North America. We sampled each waterbody in three locations at three times during the growing season, and tested which physical, chemical, and biological characteristics related to the means and variability of pCO₂ and pCH₄ in space and time. Summer means of pCO₂ and pCH₄ were inversely related to waterbody size and positively related to floating vegetative cover; pCO₂ was also positively related to dissolved phosphorus. Temporal variability in partial pressure in both gases weas greater than spatial variability. Although sampling on a single date was likely to misestimate mean seasonal pCO₂ by up to 26%, mean seasonal pCH₄ could be misestimated by up to 64.5%. Shallower systems displayed the most temporal variability in pCH₄ and waterbodies with more vegetation cover had lower temporal variability. Inland waters remain one of the most uncertain components of the global carbon budget; understanding spatial and temporal variability will ultimately help us to constrain our estimates and inform research priorities.