The replacement of native species by invasive Phragmites australis in coastal wetlands may impact ecosystem processes including fluxes of the greenhouse gases (GHGs) carbon dioxide (CO₂) and methane (CH₄). To investigate differences in daytime CH₄ and CO₂ fluxes as well as vegetation properties between Phragmites and native vegetation zones along a salinity gradient, fluxes were measured via cavity ringdown spectroscopy in 3 New England coastal marshes, ranging from oligohaline to polyhaline. While daytime CH₄ emissions decreased predictably with increasing soil salinity, those from Phragmites zones were larger (15 to 1254 μmol m⁻² h⁻¹) than those from native vegetation (4–484 μmol m⁻² h⁻¹) across the salinity gradient. Phragmites zones displayed greater daytime CO₂ uptake than native vegetation zones (−7 to −15 μmol m⁻² s⁻¹ vs. -2 to 0.9 μmol m⁻² s⁻¹) at mesohaline-polyhaline, but not oligohaline, sites. Results suggest that vegetation zone and salinity both impact net emission or uptake of daytime CO₂ and CH₄ (respectively). Future research is warranted to demonstrate Phragmites-mediated impacts on GHG fluxes, and additional measurements across seasonal and diel cycles will enable a more complete understanding of Phragmites' net impact on marsh radiative forcing.