AbstractGlobally, lakes are frequently supersaturated with carbon dioxide (CO2) and are major emitters of carbon to the atmosphere. Recent studies have generated awareness of the high variability in pCO2aq (the partial pressure corresponding to the concentration in water) and CO2 fluxes to the atmosphere and the need for better accounting for this variability. However, studies simultaneously accounting for both spatial and temporal variability of pCO2aq and CO2 fluxes in lakes are rare. We measured pCO2aq (by both manual sampling and mini loggers) and CO2 fluxes, covering spatial variability in open water areas of three lakes of different character in a Swedish catchment for 2 years. Spatial pCO2aq variability within lakes was linked to distance from shore, proximity to stream inlets, and deepwater upwelling events. Temporally, pCO2aq variability was linked with variability in dissolved organic carbon, total nitrogen, and dissolved oxygen. While previous studies over short time periods (1 to 6 h) observed gas transfer velocity (k) to be more variable than pCO2aq, our work shows that over longer time (days to weeks) pCO2aq variability was greater and affected CO2 fluxes much more than k. We demonstrate that ≥8 measurement days distributed over multiple seasons in combination with sufficient spatial coverage (≥8 locations during stratification periods and 5 or less in spring and autumn) are a key for representative yearly whole lake flux estimates. This study illustrates the importance of considering spatiotemporal variability in pCO2aq and CO2 fluxes to generate representative whole lake estimates.