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Shinnecock Bay Restoration Program

The Shinnecock Bay Restoration Program (ShiRP) was initiated by Dr. Ellen Pikitch and she and Dr. Christopher Gobler have served as co-principal investigators on the effort since 2011. It was clear then that conditions in the bay had been deteriorating over time, evidenced by excessive nitrogen loading, the presence of harmful algal blooms, a lack of shellfish, and decreasing eelgrass habitat. 


Our goal is to improve water quality within the bay through science-based in-the-water restoration focusing on key shellfish species. We are actively replenishing shellfish populations and creating more habitat and better conditions for marine life to thrive. A healthier ecosystem is also a more enjoyable environment for swimming, fishing, kayaking, sailing – just a few of the many activities that makes living on Long Island special. 


But restoring the bay is easier said than done! Our collective team of professors, students and staff at Stony Brook have spent years developing, implementing, and monitoring restoration solutions—with every strategy and activity based on scientific evidence and rigorous monitoring and evaluation. 

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Restoration Success in Shinnecock Bay

One of IOCS’s roles in ShiRP focuses on monitoring the fisheries of Shinnecock Bay. We can’t know whether our approach is benefiting the bay ecosystem unless we understand what lives there. 


Our lab uses several methods to collect data baywide, so that we can better understand the community of fish and invertebrates living in the bay, their seasonal and annual patterns, and their habitat usage. Our methods include a decade-long trawl survey, Baited Underwater Remote Video (BRUVs), and collecting water samples for environmental DNA (eDNA) analysis. By using standardized methods to survey the bay, we have a baseline of the Shinnecock Bay community and can therefore better understand changes over time and how our restoration is providing broader benefits. 


Our lab also works on communicating ShiRP’s activities to the public and key stakeholders. We frequently present to professional and local audiences and focus when we can on new community partnerships and initiatives. 

Explore our oyster reef...


million clams planted


oyster reefs built


acres of new eelgrass

Progress and Signs of Success

  • Our planted hard clams are surviving and reproducing, creating new generations of clams throughout the eastern and western parts of the bay

  • Oyster reefs are growing, and biotic communities settling onto the reefs

  • We have distributed 5 million eelgrass seeds into selected areas

  • Water quality is improving! 

    • Harmful Algae Blooms are becoming less dense and less persistent

    • Shellfish bed closures are less than half of what they were before we began restoration 

  • Eelgrass habitat is increasing in area due to better conditions and more light reaching the bottom of the bay 

  • We have seen increased biomass and species diversity in the western part of the bay as water quality and habitat have improved

  • We are discovering new species of fish due to the use of eDNA that hadn’t been observed using other methods 

Other Links


Read the news article:

SBU Scientists Take a Multi-Faceted Approach to Restoring Shinnecock Bay


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