Pleasant Bay, MA, is a 8741-ha (21,600-acre) coastal lagoon with extensive eelgrass, shellfish, and salt marsh habitats and is subject to predictable variations in inlet formation resulting in shifting tides and access to the ocean. Here we describe methods to link data from independent surveys (benthic habitat assessment and fishery-independent trawl/dredge sampling) to create linkages across the ecosystem in order to guide future monitoring and management efforts.. The integration of water parameters, grain size, and surficial benthic analysis to create habitat categories allowed us to explain 45% of microinvertebrate distribution. Microinvertebrate communities had significant correlations to fish and macroinvertebrate communities, strengthening the usefulness of microinvertebrate surveys. Habitat categories containing Zostera marina (Common Eeelgrass) had higher species diversity and abundances of fishes and macroinvertebrates than other habitats. The links between habitat, communities of microinvertebrates, macroinvertebrates, and fish indicate a connected ecosystem.