To improve fossil fuel CO2 emissions estimates, high spatial and temporal resolution inventories are replacing coarse resolution, annual-mean estimates distributed by population density. Because altering the emissions changes a key boundary condition to inverse-estimated CO2 fluxes, it is essential to analyse the atmospheric impacts of redistributing anthropogenic emissions. Using a coupled ecosystem–atmosphere model, we compare 2004 atmospheric CO2 concentrations resulting from coarse and high-resolution inventories. Using fossil fuel CO2 emissions inventories with coarse spatial and temporal resolution creates spatially coherent biases in the atmospheric CO2 concentrations. The largest changes occur from using seasonally varying emissions: in heavily populated areas along the west coast and the eastern United States, the amplitude of the near-surface CO2 concentration seasonal cycle changed by >10 ppm, with higher concentrations in summer and lower concentrations in fall. Due to changes in the spatial distribution, spatially coherent annual mean concentration differences >6 ppm occur; and including the diurnal cycle causes changes >3 ppm. To avoid significant errors in CO2 source and sink estimates from atmospheric inversions, it is essential to include seasonality in fossil fuel emissions, as well as to utilize higher-resolution, process-based spatial distributions.