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Biscayne Bay Habitat Focus Area

Developing a scientific basis for good resource management in the Biscayne Bay Habitat Focus Area.

In 2015 the Biscayne Bay Habitat Focus Area was designated. It included Biscayne Bay and its adjacent reef tract, including all of Biscayne National Park, the Florida DEP Biscayne Bay Aquatic Preserves, and the northern extension of the Florida Keys National Marine Sanctuary beyond the US Highway 1 bridge at Manatee Bay. 

The designation created a nucleus of NOAA resources to attract partners from state and local governmental agencies and nongovernmental entities into productive partnerships to fight for the Area’s wellbeing against multiple growing threats. 

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Different Biscayne Bay environments, both to benefit from the designation of Habitat Focus Area.




The Implementation Plan for the Biscayne Bay Habitat Focus Area (HFA), prepared by NOAA and potential partners, is directed at four goals, as follows: 1) improving water quality, 2) securing and maintaining sufficient freshwater inflow into the bay, 3) protecting and improving habitat for protected and fishery resources that use the bay and reef tract, and 4) generating a strong, well informed constituency. The Biscayne Bay HFA’s approaches to achieving these goals are to develop a scientific basis for good resource management and to use education and outreach activities to inform and provide incentives to policy makers and the public to generate both voluntary and mandated actions to improve bay habitat.


SCUBA Diver retrieving equipment.


Three senior scientists at local NOAA labs, the Southeast Fisheries Science Center (SEFSC) Miami Laboratory of NOAA Fisheries and the Atlantic Oceanographic and Meteorological Laboratory of NOAA Oceanic and Atmospheric Research, are leading the Biscayne Bay HFA. Working with professors and students at the University of Miami and other institutions, they have been generating scientific papers that can be the basis of guidance documents. Miami Waterkeeper, with competitive funding from the NOAA HFA initiative for five years, has been conducting education and outreach as well as developing and dispensing Best Management Practice guidance documents, reporting apparent regulatory violations, leading guided trips on the Bay for government and civic leaders, and training high-school-level young people in distribution of environmental information.


Habitat Focus Area accomplishments depend upon forming good partnerships, and this is nowhere truer than for the Biscayne Bay HFA. Partnerships of the SEFSC and AOML scientists leading the Biscayne Bay HFA with governmental and institutional neighbors have led directly to the publication of three refereed papers related to water quality in Biscayne Bay, the formation of a spatially comprehensive acoustic array (part of the FACT [Florida Atlantic Cooperative Telemetry] network), and the acoustic detection of 10 acoustically tagged endangered smalltooth sawfish by the acoustic array since 2015, as well as the addition of documented historic records on sawfish encounters within the area of the Biscayne Bay HFA, reported for the first time to the International Sawfish Encounter Database. A landscape-scale study is underway in a major waterway discharging nutrients to the Bay that are promoting eutrophication, a process where a body of water becomes enriched in dissolved nutrients which may in turn deplete dissolved oxygen. This study will provide a model for conducting similar studies in canals to be identified as other important nutrient conduits.

Specific funding from NOAA for the Biscayne Bay HFA ends in 2020, but local sponsors plan to continue efforts to protect and promote the ecological wellbeing of Biscayne Bay under the Biscayne Bay HFA umbrella. Continuation is well worth it because Biscayne Bay and its parallel reef tract are economic engines that will keep on giving to the South Florida region if their ecological integrity and ecosystem health are reestablished and maintained.


Majewska, R., Bosak S., Frankovich, T.A., Ashworth, M.P., Sullivan, M.J., Robinson, N.J., Lazo-Wasem, E.A., Pinou, T., Nel. R., Manning, S.R., and Van de Vijver, B. (2019) Six new epibiotic Proschkinia (Bacillariophyta) species and new insights into the genus phylogeny. European Journal of Phycology Volume 54, 2019 Issue 4, 609-631. DOI:https://doi.org/10.1080/09670262.2019.1628307

Wachnicka, A., Browder, J., Jackson, T., Louda, W., Kelble, C., Abdelrahman, O., Stabenau, E., and Avila, C. Hurricane Irma's Impact on Water Quality and Phytoplankton Communities in Biscayne Bay (Florida, USA). Estuaries and Coasts 43: 1217-1234 (2020). DOI: https://doi.org/10.1007/s12237-019-00592-4

Zink, I.C., Jackson,T.L., and Browder, J.A. 2018. A Note on the Occurrence of Non-Native Tiger Prawn (Penaeus monodon Fabricius, 1798) in Biscayne Bay, FL, USA and Review of South Florida Sighting and Species Identification. BioInvasions Records (2018) Volume 7, Issue 3: 297-302. DOI: https://doi.org/10.3391/bir.2018.7.3.11

Laura H. McDonnell, Thomas L. Jackson, George H. Burgess, Lindsay Phenix, Austin J. Gallagher, Helen Albertson, Neil Hammerschlag, Joan A. Browder. 2020. Saws and the city: smalltooth sawfish (Pristis pectinata) encounters, recovery potential and research priorities in urbanized coastal waters off Miami, Florida. Endangered Species Research 43:543-553. DOI: https://doi.org/10.3354/esr01085

Our Partners

Biscayne Bay Regional Restoration and Coordination Team, Miami-Dade County, Florida Department of Environmental Protection, Biscayne Bay Aquatic Preserves, Biscayne National Park, Miami Waterkeeper, Florida Sea Grant, Tropical Audubon Society, Clean Water Action, National Parks Conservation Association, University of Miami, Florida International University

Learn more about additional NOAA Habitat Focus Areas

Last updated by Southeast Fisheries Science Center on February 22, 2022