Our study of a St. Lawrence Estuary marsh reveals that, compared to native Spartina patens‐dominated vegetation, invasive Phragmites australis makes a greater contribution to soil volume and carbon stock (referred to as blue carbon). Phragmites' contributions to soil volume enhance marsh sustainability in face of sea level rise, and its greater contribution to soil carbon helps to reduce the atmospheric concentration of CO2. Phragmites australis (common reed) is a cosmopolitan species growing in fresh to brackish wetlands. An invasive genetic strain, introduced from Europe or Asia, has expanded extensively along the St. Lawrence River in the last few decades but has been little studied on the estuarine portion. We collected soil cores from three sites within an invasive Phragmites stand and one site within S. patens‐dominated stand in a St. Lawrence Estuary salt marsh near la Pocatiere, Quebec. We measured the bulk density, carbon content, volume, and mass of belowground organic matter in 2‐cm‐thick soil layers of three cores at each Phragmites site. Bulk density and carbon content were measured in 5‐cm‐thick soil layers of three cores at S. patens site. Results showed that soil in the Phragmites stands held 37–77% more blue carbon than in the S. patens‐dominated marsh. Based upon their diameter size, Phragmites rhizomes could be contributing 7.4–10.2 cm to the thickness in the upper 20 cm of soil. We suggest that any management of invasive Phragmites include consideration of its role in increasing blue carbon stocks and marsh resilience along with other ecosystem services. Plain Language Summary An aggressive invasive strain of the common reed (Phragmites australis) is widespread on the eastern coast of North America. It is rapidly spreading through salt marshes, the grassy meadows, which straddle mean sea level on the coast of Quebec's St. Lawrence Estuary. This reed is considered to degrade the value of the native salt marsh and its biodiversity by displacing native vegetation and the habitat it provides for birds and wildlife such as the Nelson's Sparrow, designated as a Species of Special Concern in nearby Maine. Our study of a St. Lawrence salt marsh, however, shows that the invasive reed can have positive effects on soil properties. We compared soils below the reed and the most common native grass, salt meadow hay (Spartina patens) and found 37–77% more carbon stored in the reed soil. Thus, growth of the reed increases the ability of salt marshes to reduce concentrations of atmospheric carbon dioxide and mitigate climate change. We measured how much the roots and rhizomes (underground stems) of the two species contributed to the soil volume and found that the reed contributed considerably more. Greater contributions to soil volume means that the elevation of the soil surface will increase faster in the reed marsh and help this tidal ecosystem to keep up with increased rates of sea level rise that will accompany climate warming. Thus, any management of the invasive reed should include consideration of its role in mitigation of climate change and marsh adaptation to sea level rise, along with other ecosystem values provided by the native vegetation. Key Points Phragmites australis has invaded Spartina patens‐dominated marshes of the St. Lawrence Estuary Soils of invasive Phragmites had 37–77% greater C stocks than S. patens soils Phragmites contributed 7.4–10.2 cm to the thickness of the top 20 cm of soil