Understanding the carbon dioxide and water fluxes in the Arctic is essential for accurate assessment and prediction of the responses of these ecosystems to climate change. In the Arctic, there have been relatively few studies of net CO2, water, and energy exchange using micrometeorological methods due to the difficulty of performing these measurements in cold, remote regions. When these measurements are performed, they are usually collected only during the short summer growing season. We established eddy covariance flux towers in three representative Alaska tundra ecosystems (heath tundra, tussock tundra, and wet sedge tundra), and have collected CO2, water, and energy flux data continuously for over three years (September 2007–May 2011). In all ecosystems, peak CO2 uptake occurred during July, with accumulations of 51–95 g C/m2 during June–August. The timing of the switch from CO2 source to sink in the spring appears to be regulated by the number of growing degree days early in the season, indicating that warmer springs may promote increased net CO2 uptake. However, this increased uptake in the spring may be lost through warmer temperatures in the late growing season that promote respiration, if this respiration is not impeded by large amounts of precipitation or cooler temperatures. Net CO2 accumulation during the growing season was generally lost through respiration during the snow covered months of September–May, turning the ecosystems into net sources of CO2 over measurement period. The water balance from June to August at the three ecosystems was variable, with the most variability observed in the heath tundra, and the least in the tussock tundra. These findings underline the importance of collecting data over the full annual cycle and across multiple types of tundra ecosystems in order to come to a more complete understanding of CO2 and water fluxes in the Arctic.