Coastal salt marshes are essential for climate change mitigation due to their high carbon storage capacity, which is influenced by soil type, hydrology, and floristic composition. Over the past century, invasive Phragmites australis has displaced native Spartina alterniflora across salt marshes on the Long Island Sound, and it is widely hypothesized that its larger biomass and rapid growth enhance soil carbon sequestration. This study tested that hypothesis by comparing TOC stocks and physical soil properties in two southern Connecticut marshes over multiple seasons. Our results show that mean soil bulk density was significantly higher under P. australis than S. alterniflora at both locations. However, this did not translate to superior carbon storage. Analysis showed significant seasonal effect but no significant overall difference in median TOC between species, indicating that P. australis is competitive in total mass only due to its higher soil density. Notably, Levene’s test for homogeneity of variance was significant (P = 0.039), revealing that P. australis creates highly heterogeneous "hot spots" of carbon storage compared to the relatively uniform distribution found in native stands. These findings suggest that while P. australis invasion results in a more physically dense and potentially resilient marsh platform—relevant for surviving sea-level rise and filtering nutrient runoff—it may simultaneously compromise the stability and uniformity of regional carbon sinks. Management strategies should consider these tradeoffs when prioritizing the protection of native S. alterniflora for consistent carbon sequestration.