Abiotic global change factors, such as rising atmospheric CO2, and biotic factors, such as exotic plant invasion, interact to alter the function of terrestrial ecosystems. An invasive lineage of the common reed, Phragmites australis, was introduced to North America over a century ago, but the belowground mechanisms underlying Phragmites invasion and persistence in natural systems remain poorly studied. For instance, Phragmites has a nitrogen (N) demand higher than native plant communities in many of the ecosystems it invades, but the source of the additional N is not clear. We exposed introduced Phragmites and native plant assemblages, containing Spartina patens and Schoenoplectus americanus, to factorial treatments of CO2 (ambient or +300 ppm), N (0 or 25 g m−2 year−1), and hydroperiod (4 levels), and focused our analysis on changes in root productivity as a function of depth and evaluated the effects of introduced Phragmites on soil organic matter mineralization. We report that non-native invasive Phragmites exhibited a deeper rooting profile than native marsh species under all experimental treatments, and also enhanced soil organic matter decomposition. Moreover, exposure to elevated atmospheric CO2 induced a sharp increase in deep root production in the invasive plant. We propose that niche separation accomplished through deeper rooting profiles circumvents nutrient competition where native species have relatively shallow root depth distributions; deep roots provide access to nutrient-rich porewater; and deep roots further increase nutrient availability by enhancing soil organic matter decomposition. We expect that rising CO2 will magnify these effects in deep-rooting invasive plants that compete using a tree-like strategy against native herbaceous plants, promoting establishment and invasion through niche separation.