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.