Many compelling management issues in Long Island Sound (LIS) focus on how organisms respond to stresses such as commercial and recreational harvesting, eutrophication, hypoxia, habitat degradation, invasion of non-native species, ocean acidification, and climate change. In order to address these complex problems, we must first understand the factors controlling biological processes and how organisms interact ecologically. This chapter provides an overview of the major groups of organisms occupying the dominant habitats of LIS.