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Accounting for temporal changes in carbon dioxide (CO₂) effluxes from freshwaters remains a challenge for global and regional carbon budgets. Here, we synthesize 171 site-months of flux measurements of CO₂ 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 CO₂ flux at all sites. By accounting for diel variation, only 11% of site-months were net daily sinks of CO₂. Annual CO₂ emissions had an average of 25% (range 3%-58%) interannual variation. Similar to studies on streams, nighttime emissions regularly exceeded daytime emissions. Biophysical regulations of CO₂ flux variability were delineated through mutual information analysis. Sample analysis of CO₂ 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 CO₂ 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.