Interest in leveraging suspension feeders, such as marine bivalves, to exert top‐down control on organic matter (OM) loading in estuaries is gaining momentum. Not only can these faunal engineers alleviate the consequences of nutrient pollution, but they may also bolster the critical blue carbon services provided by coastal ecosystems—a potential dual, mitigating effect on cultural eutrophication and climate change. Ribbed mussels, Geukensia demissa, offer a useful model for assessing faunally driven carbon (C) and nitrogen (N) processes in these systems and their relationships with faunal density. Combining bulk geochemical analyses with Bayesian stable isotope mixing model frameworks (MixSIAR), we quantified the effect of mussels on the source and amount of organic C and N deposited to the benthic floor (i.e., sedimentation), accumulated in surface sediments, and stored in aboveground Spartina alterniflora in Georgia salt marshes. Relative to areas without mussels, mussel presence shifted the source of deposited and accumulated OM to a more allochthonous makeup; amplified the amount of deposited, but not accumulated, allochthonous and autochthonous OM; and enhanced aboveground storage of C and N. Both sources of OM accumulated in sediments as well as standing stocks of C and N were highly and positively correlated with local mussel density (ind. m−2) but unrelated to neighboring mussel density (ind. ∼25 m−2) in adjacent, non‐mussel areas. This work provides new evidence that suspension feeders, through their faunal engineering activities, can interact powerfully and synergistically with primary producers to enhance the blue carbon services of marshes and counteract coastal eutrophication.