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Abstract Accounting for temporal changes in carbon dioxide (CO ₂ ) effluxes from freshwaters remains a challenge for global and regional carbon budgets. Here, we synthesize 171 site-months of flux measurements of CO ₂ based on the eddy covariance method from 13 lakes and reservoirs in the Northern Hemisphere, and quantify dynamics at multiple temporal scales. We found pronounced sub-annual variability in CO ₂ flux at all sites. By accounting for diel variation, only 11% of site-months were net daily sinks of CO ₂ . Annual CO ₂ emissions had an average of 25% (range 3%–58%) interannual variation. Similar tomore » studies on streams, nighttime emissions regularly exceeded daytime emissions. Biophysical regulations of CO ₂ flux variability were delineated through mutual information analysis. Sample analysis of CO ₂ fluxes indicate the importance of continuous measurements. Better characterization of short- and long-term variability is necessary to understand and improve detection of temporal changes of CO ₂ fluxes in response to natural and anthropogenic drivers. Our results indicate that existing global lake carbon budgets relying primarily on daytime measurements yield underestimates of net emissions.« less