In our companion manuscript we identified 11 waterbirds as indicators of various pressures on the coastal marine ecosystems of southern Florida. Here, we identify the habitats on which these species depend and the ecological linkages that make them representative of those habitats. Through the use of conceptual ecological models (CEMs), we develop tools that can be used by managers/decision makers to evaluate the health of the various habitats in order to rectify myriad problems that are occurring or will possibly occur in the future such that the valuable ecosystem services provided by these habitats can be maximized. We also demonstrate the practical use of these tools by documenting data availability, benchmarks, and scientific needs for each species.