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Measuring the Restoration

Environmental monitoring plays a foundational role in our restoration efforts. It is a critical tool to inform project design and evaluate restoration success. Targeted and consistent monitoring provides us with the data we need to assess whether our goals have been met, tells us how we are doing along the way, and provides information that allows us to take an “adaptive management” approach. This wealth of information, when looked at holistically, also facilitates the formation of new questions and future directions. 

A simplified way of looking at our monitoring efforts is to think about them in two ways:

Measuring Restoration
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Monitoring the Restoration

“direct” monitoring


Monitoring helps us quantify the restoration impact. Without such surveys and data collection, it would be impossible to know if the planted clams are surviving and reproducing, whether oyster shellbags are becoming healthy reefs, or if eelgrass seed dispersal is resulting in new healthy meadows

Monitoring the Ecological Effects & Impacts

“broad” monitoring


Monitoring also helps us measure broader ecological impacts resulting from restoration activities. Are the millions of new shellfish filtering the bay enough to significantly improve water quality? Are the shellfish producing new recruits outside the restoration areas and replenishing clams and oysters throughout the bay? Are the restoration efforts resulting in positive impacts to higher trophic levels like fish, invertebrates, elasmobranchs, or marine mammals? 

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Monitoring the Ecological Effects & Impacts

Monitoring the Restoration

Water Quality 

➔ Continuous Water Sampling: Tracking nitrogen, chlorophyll, oxygen, pH, and harmful algal bloom (HAB) densities.

➔ Clarity Checks: Utilizing Secchi disks to gauge water transparency.


➔ Clam Health: Examining planted clams for survival rates and breeding activity.

➔ Population recruitment: Detecting the presence of new clams and oysters throughout the extent of the bay, and measuring clam population increases

➔ Spat-on-Shell Surveillance: Monitoring oyster growth, mortality, and disease prevalence.


➔ Biodiversity Barometer: Employing fishery surveys and environmental DNA (eDNA) to characterize species abundance and diversity.

➔ Seasonal Shifts: Identifying seasonal and temporal patterns.

➔ Predictive Ecosystem Modeling: Developing models to forecast ecological shifts.


➔ Eelgrass Expansion: Applying diver surveys and machine learning to quantify eelgrass increases.

➔ Reef Residency: Evaluating fish and biodiversity through traps and eDNA analysis on oyster reefs.

How and what are we evaluating?

Ecosystem Monitoring

Examples of Monitoring in Practice

Examples of Monitoring
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Example 1:
Pre-Restoration Surveys and Experiments

Before any restoration began, we conducted field surveys and experiments to understand which species to use, how likely they were to grow and survive under stressful real world conditions (e.g. high temperatures, low oxygen, low pH, high HAB densities), and which locations were most suitable for restoration. 

  • Testing different life stages of clams, oysters and scallops in the laboratory to assess resilience 

  • Deploying oysters into seven different bay locations to see where growth rates were highest and mortality rates were lowest 

  • Surveying bottom type to determine habitat suitability for hard clams

  • Developing a water circulation model to more accurately project areas of new recruitment and to ensure larvae would not be flushed out to see with tidal flow.

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Example 2:
Benthic Sampling

Benthic sampling, put simply, is measuring the conditions and marine life of the seafloor. Because hard clams, oyster reefs, and eelgrass reside on the seafloor, it is important to understand things like sediment type, species abundance and diversity, and nutrient content. Benthic sampling can also focus specifically on one species, to capture information such as numbers of individuals or reproductive condition. Our benthic sampling has allowed us to collect information on many important indicators, including: 

  • The condition of hard clams once they are planted, to determine if they are surviving and if they are in good reproductive condition.

  • The number of clams inside the sanctuaries, to determine if there is any significant mortality or poaching. 

  • Evidence of recruitment outside the sanctuaries, to measure how many new clams the spawner sanctuaries have produced. 

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Example 3:
Water Sampling

Water samples can provide a wealth of information that answer both specific and broad questions. We use water samples to collect data on physical parameters (temperature, turbidity, salinity, and dissolved oxygen), chemical parameters (nutrient concentrations such as nitrogen; chlorophyll, pH), biological indicators (presence and abundance of harmful algae, larvae, etc.), and ecosystem indicators (biodiversity snapshots via eDNA). Water sampling has enabled us to understand how the biological restoration has resulted in broader environmental improvements:

  • Decreasing concentrations of Brown, red, and rust tides, and eliminating brown tide blooms 

  • Reduction in nitrogen levels

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Fisheries Monitoring

In order to capture how the restoration is benefiting Shinnecock Bay as a whole, we monitor broader elements of the ecosystem, including biodiversity. Fisheries surveys enable us to determine species composition, seasonal patterns, and changes over time.

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