Accounting for temporal changes in carbon dioxide (CO₂) emissions from freshwaters remains a challenge for global and regional carbon budgets. Here, we synthesize 171 site-months of eddy covariance flux measurements of CO₂ from 13 lakes and reservoirs in the Northern Hemisphere (NH) and quantify dynamics at multiple temporal scales. We found pronounced sub-annual variability in CO₂ flux at all sites. 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. Nighttime emissions regularly exceeded daytime emissions. Sources of CO₂ flux variability were delineated through mutual information analysis. Sample analysis of CO₂ fluxes indicate importance of continuous sampling. Constraining short- and long-term variability is necessary to improve detection of temporal changes of CO₂ fluxes in response to natural and anthropogenic drivers.