Bay scallops, Argopecten irradians, supported vibrant fisheries which subsequently collapsed, as such, they are a focus species for many restoration efforts along the Atlantic and Gulf coasts of the United States. The scallops’ preferred habitat, seagrass, has also dramatically declined, and some scallop populations have increased post-restoration despite reduced seagrass cover. This has led to the hypothesis that macroalgae may serve as suitable alternative habitats for bay scallops. This study is the first to compare demographic rates, such as long-term survival, growth, condition and reproductive potential of scallops between the native eelgrass, Zostera marina, and the introduced alga, Codium fragile. Although long-term survival was not different between habitats, results suggest site-specific and inter-annual variation in the impacts of Codium on scallop growth. While demographic rates did not differ in Shinnecock Bay, in Sag Harbor, growth and/or condition were significantly different between both vegetated habitats depending on the year. However, recruit density, size and condition did not vary significantly, adding to the complexity of this relationship. Despite potential site-specific and inter-annual differences, this study supports the hypothesis that habitats other than eelgrass can benefit bay scallops.