||Anthropogenically induced changes to estuaries, including shifts from seagrass to macroalgae-dominated habitats, have led to concerns about the ability of estuaries to support fish and invertebrates. To assess differences in habitat quality of seagrass and macroalgae, we examined faunal community structure and consumer carbon assimilation in adjacent areas of seagrass, macroalgae, and bare sediments in Sage Lot Pond, Waquoit Bay, MA. Vegetation was an important factor controlling abundances, and both seagrass and macroalgae provided suitable habitat for a range of benthic fauna. Differences in consumption and assimilation of carbon of seagrass and macroalgal origin were demonstrated by shifts in delta13C values of consumers between the seagrass meadow and adjacent macroalgal mats. Overall, consumers generally reflected incorporation of carbon from the dominant producers in the habitat where they were collected although macroalgae was an important carbon source for organisms in this study. These results revealed differences in carbon flow from producers to consumers across very small spatial scales (lt;10 m) within an estuary.