Most U.S. commercial fisheries landing consists of species dependent on coastal estuaries for spawning, nursery, or migratory feeding habitat. Loss of wetlands, anthropogenic contamination, eutrophication, and hypoxia all threaten the coastal habitats that many living marine resources (LMRs) require. Despite a clear connection between coastal habitat and fisheries, significant gaps exist in our knowledge of how the nearshore environment is utilized by many species and how its quality affects recruitment success. A comparative research approach is proposed to identify critical habitats in the northeast U.S. for several LMRs, including winter flounder (Pleuronectes americanus), summer flounder (Paralichthys dentatus), tautog (Tautoga onitis), and black sea bass (Centropristis striata). EMphasis is on following cohorts throughout their first year, so that population level effects may be investigated. A goal of this approach is to compare the functional significance of specific habitat-types among three estuarine systems in the mid-Atlantic and southern New England which support similar species assemblages but differ in the extent of anthropogenic disturbance.