These water quality data are one of many studies being done to assess and monitor coral reef ecosystems.The intent of this work is three fold: (1) to spatially characterize and monitor the distribution, abundance, and size of both reef fishes and macro-invertebrates (conch, lobster, Diadema); (2) to relate this information to in-situ data collected on water quality and associated habitat parameters; (3) to use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting and to establish the efficacy of those management decisions. Toward this end, the Center for Coastal Monitoring and Assessment's Biogeography Branch (BB) has completed its fourth year and is beginning its fifth year of work in the US Virgin Islands and Puerto Rico. It is critical, with recent changes in management at both locations (e.g. implementation of MPAs) as well as proposed changes (e.g. zoning to manage multiple human uses) that action is taken now to accurately describe and characterize the fish/macro-invertebrate populations in these areas. It is also important that BB work closely with the individuals responsible for recommending and implementing these management strategies. Recognizing this, BB has been collaborating with partners at the University of Puerto Rico, National Park Service, US Geological Survey and the Virgin Islands Department of Planning and Natural Resources.To quantify patterns of spatial distribution and make meaningful interpretations, we must first have knowledge of the underlying variables determining species distribution. The basis for this work therefore, is the nearshore benthic habitats maps (less than 100 ft depth) created by NOAA's Biogeography Program in 2001 and NOS' bathymetry models. Using ArcView GIS software, the digitized habitat maps are stratified to select sampling stations. Sites are randomly selected within these strata to ensure coverage of the entire study region and not just a particular reef or seagrass area. At each site, fish, macro-invertebrates, and associated water quality and habitat information is then quantified following standardized protocols. By relating the data collected in the field back to the habitat maps and bathymetric models, BB is able to model and map species level and community level information. These protocols are standardized throughout the US Caribbean to enable quantification and comparison of reef fish abundance and distribution trends between locations. Armed with the knowledge of where "hot spots" of species richness and diversity are likely to occur in the seascape, the BB is in a unique position to answer questions about the efficacy of marine zoning strategies (e.g. placement of no fishing, anchoring, or snorkeling locations), and what locations are most suitable for establishing MPAs. Knowledge of the current status of fish/macro-invertebrate communities coupled with longer term monitoring will enable evaluation of management efficacy, thus it is essential to future management actions.