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 the magnitude and dynamics at multiple temporal scales. We found pronounced diel and sub-monthly oscillatory variations in CO₂ flux at all sites. Diel variation converted sites to daily net sinks of CO₂ in only 11% of site-months. Upscaled annual emissions had an average of 25% (range 3-58%) interannual variation. Given temporal variation remains under-represented in inventories of CO₂ emissions from lakes and reservoirs, revisions in CO₂ flux are needed using a better representation of sub-daily to interannual variability. Constraining short- and long-term variability is necessary to improve detection of temporal changes of CO₂ fluxes in response to natural and anthropogenic drivers.