Static chamber fluxes of carbon dioxide and methane from Phragmites wetlands and supporting data collected across a salinity gradient on Cape Cod, Massachusetts. Measurements of carbon dioxide and methane fluxes from static chambers were collected to assess carbon exchange at four coastal Phragmites wetland sites across a salinity gradient (4 to 25 psu) in impounded and natural, tidally unrestricted Phragmites wetlands at the Herring River in Wellfleet, MA, USA and at Sage Lot Pond in Waquoit, MA from July through November 2020.