In much of the USA, Phragmites australis is a prolific invasive species in wetland habitats. The spread of Phragmites can significantly alter the structure and function of a marsh, thereby altering the ecosystem services that the marsh provides. It remains unclear how Phragmites invasion may impact coastal protection, despite the substantial implications for local communities. Here, we investigated the ability of a Phragmites marsh to attenuate waves via long-term field monitoring and compared this to native Spartina alterniflora via hydrodynamic modeling. Phragmites was capable of attenuating incoming waves and did so most effectively at higher stem densities and lower water levels. Under no conditions studied here did Phragmites attenuate waves more than S. alterniflora. During the summer and fall as well as during lower water levels, Phragmites significantly underperformed S. alterniflora. This indicates that Phragmites invasion may conditionally increase the coastal hazard facing local communities, and highlights that Phragmites management should be coupled with the restoration of native species.