We characterized the tundra vegetation at three eddy covariance towers located along a toposequence in northern Alaska and studied seasonal variations in plot-level CO2 fluxes among the dominant vegetation types with chambers during the summer and with the gradient-diffusion technique during the winter. We performed footprint analyses to determine the source areas contributing to the tower fluxes and scaled plot-level to eddy-covariance CO2 data based on the proportion of vegetation types occurring within the footprints. At peak growing season, both gross ecosystem exchange and ecosystem respiration were greater in moist acidic tussock tundra and wet sedge tundra than in dry heath tundra. This resulted in relatively similar values of net ecosystem exchange as measured by chambers in July in tussock tundra across all topographic positions and wet sedge tundra (−2.4 to −4.2 μmol CO2/m2/s) but low values in dry heath tundra (−0.4 μmol CO2/m2/s). Winter respiration was highest for tussock tundra in December, but there were no significant differences among vegetation types in February and April. Net and gross ecosystem exchange scaled up from summer chamber measurements compared well to tower data (r2 = 0.84 and r2 = 0.78, respectively), especially on level terrain, whereas plot-level CO2-flux measurements in the winter did not agree well with tower data. This is one of few studies to compare plot-level and tower fluxes during both summer and winter and to demonstrate successful upscaling of carbon exchange in Arctic tundra systems under certain conditions.