The project originated from an ongoing collaboration between USDA (U.S. Department of Agriculture) and NOAA on the U.S. Coral Reef Task Force. The Conservation Effects Assessment Project (CEAP) was developed in 2003 by the USDA as a multi-agency effort to quantify the environmental benefits of conservation practices applied by private landowners. Ten Special Emphasis Watersheds (SEW) were identified throughout the U.S. to address specific resource concerns such as animal feeding operations, water use, drainage management and wildlife habitat restoration. The Jobos Bay watershed was selected by CEAP partners as the first tropical CEAP SEW with the goal of identifying innovative conservation practices that will enhance the health of coral reef ecosystems. The project's general approach includes describing the baseline conditions in Jobos Bay, implementing agricultural conservation practices on the watershed and measuring the response in Jobos BayÕs water quality, biogeochemistry, benthic habitats and marine biota. It is anticipated that relatively short term changes will be measured in water quality and marine sediments; while long-term changes in higher trophic levels, such as fishes, may be detected in out-years. The baseline biological monitoring was conducted in June 2009 by the Center for Coastal Monitoring and Assessment's Biogeography Branch. Biogeography Branch staff used monitoring protocols developed under NOAA's Caribbean Coral Reef Ecosystem Monitoring Project, which have been used since 2001 to monitor fish and benthic habitats in Puerto Rico and the U.S. Virgin Islands. These protocols are standardized throughout the US Caribbean to enable quantification and comparison of reef fish abundance and distribution trends between locations. Specific objectives were: (1) to spatially characterize and monitor the distribution, abundance, and size of both reef fishes and macro-invertebrates (conch, lobster and sea urchin), (2) to relate this information to in situ data collected on associated benthic composition parameters, (3) to use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting, and (4) to establish the efficacy of those management decisions. Using ArcView GIS software, nearshore benthic habitat maps created by NOAA's BB in 2001 were stratified to select sampling stations. Sites were 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 benthic composition information were 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.