Understanding methane emissions from natural sources is becoming increasingly important with future climactic uncertainty. Wetlands are the single largest natural source of methane; however, little attention has been given to how biota and interactions between aboveground and belowground communities may affect methane emission rates in these systems. To investigate the effects of vegetative disturbance and belowground biogeochemical alterations induced by biota on methane emissions in situ, we manipulated densities of Littoraria irrorata (marsh periwinkle snails) and Geukensia granosissima (gulf ribbed mussels) inside fenced enclosures within a Spartina alterniflora salt marsh and measured methane emissions and sediment extracellular enzyme activity (phosphatase, β-glucosidase, cellobiohydrolase, N-acetyl-β-D-glucosaminidase, peroxidase, and phenol oxidase) over the course of a year. Changes in snail density did not have an effect on methane emission; however, increased densities of ribbed mussels significantly increased the emission of methane. Sediment extracellular enzyme activities for phosphatase, cellobiohydrolase, N-acetyl-β-D-glucosaminidase, and phenol oxidase were correlated to methane emission, and none of the enzymes assayed were affected by the snail and mussel density treatments. While methane emissions from salt marsh ecosystems are lower than those from freshwater systems, the high degree of variability in emission rates and the potential for interactions with naturally occurring biota that increase emissions warrant further investigations into salt marsh methane dynamics.