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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 CO₂and 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 ofpCO₂andpCH₄in space and time. Summer means ofpCO₂andpCH₄were inversely related to waterbody size and positively related to floating vegetative cover;pCO₂was 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 seasonalpCO₂by up to 26%, mean seasonalpCH₄could be misestimated by up to 64.5%. Shallower systems displayed the most temporal variability inpCH₄and 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.

Lakes process both terrestrial and aquatic organic matter, and the relative contribution from each source is often measured via ecosystem metabolism and terrestrial resource use in the food web (i.e., consumer allochthony). Yet, ecosystem metabolism and consumer allochthony are rarely considered together, despite possible interactions and potential for them to respond to the same lake characteristics. In this study, we compiled global datasets of lake gross primary production (GPP), ecosystem respiration (ER), and zooplankton allochthony to compare the strength and shape of relationships with physicochemical characteristics across a broad set of lakes. GPP was positively related to total phosphorus (TP) in lakes with intermediate TP concentrations (11–75 μg L⁻¹) and was highest in lakes with intermediate dissolved organic carbon (DOC) concentrations. While ER and GPP were strongly positively correlated, decoupling occurred at high DOC concentrations. Lastly, allochthony had a unimodal relationship with TP and related variably to DOC. By integrating metabolism and allochthony, we identified similar change points in GPP and zooplankton allochthony at intermediate DOC (4.5–10 mg L⁻¹) and TP (8–20 μg L⁻¹) concentrations, indicating that allochthony and GPP may be coupled and inversely related. The ratio of DOC:nutrients also helped to identify conditions where lake organic matter processing responded more to autochthonous or allochthonous organic matter sources. As lakes globally face eutrophication and browning, predicting how lake organic matter processing will respond requires an updated paradigm that incorporates nonlinear dynamics and interactions.