Our monitoring program provides baseline data to help track changes in the environment, identify new threats, and assess the effectiveness of management actions. We support and manage efforts to monitor water quality, habitats, and species throughout the Great Bay Estuary. With our partners, we work to ensure the data we collect is valuable at multiple scales and can be compared to other environmental datasets. We also participate in the NERRS System-Wide Monitoring Program (SWMP), a national effort that engages all Reserves in tracking weather, water quality, and habitat conditions with a standardized approach to data collection, analysis, and management. As a result, our data can be used locally and in regional and national comparisons of estuarine conditions.

Water Quality

In partnership with the University of New Hampshire’s (UNH) Jackson Estuarine Laboratory, we operate four SWMP water quality stations (map), each outfitted with a datasonde that records temperature, depth, salinity, turbidity, pH, and dissolved oxygen every 15 minutes. We also track dissolved inorganic nutrients, suspended solids, particulate organic matter, and chlorophyll-a monthly at each location. We monitor the same parameters at frequent intervals over a full tidal cycle on the Lamprey River. All of this data is submitted to the Central Data Management Office and the New Hampshire Department of Environmental Services.

Annual Water Quality Report Cards

2022 Report Card
2021 Report Card
2020 Report Card
2019 Report Card


A weather station in Greenland provides contextual information to interpret water quality data. It collects data on temperature, precipitation, barometric pressure, relative humidity, photosynthetically active radiation (PAR), and wind speed and direction. Water quality and weather data are telemetered in near real-time so users can track changes in the environmental conditions. This data is available at the Centralized Data Management Office.


We monitor key estuarine habitats through geospatial mapping and biological surveys. Our staff is working with NOAA’s Office for Coastal Management to develop high resolution coastal wetland habitat maps for New Hampshire. These will form the basis of a new landscape scale assessment of marsh condition and resilience, help prioritize field monitoring, and inform models to predict how habitats will shift. Using transects and quadrats, our staff and volunteers also monitor saltmarsh health each summer. They look at what type of vegetation is growing, how the upland edge of the marsh is changing, and other environmental changes we expect from sea level rise. We also partner to monitor mudflats, eelgrass, and oyster beds.


Working with UNH and agency partners, we monitor macroalgae, periphyton, crabs, and horseshoe crabs. Reserve lands and waters also host other studies of species like saltmarsh sparrows, anadromous fish, or Blanding’s Turtles. Some of these are efforts to understand emerging threats to our estuary; others are tracking the health of specific species over time.

Water Levels

We partner with NOAA to host a high accuracy tide station at the southern end of Great Bay. Having detailed information about water levels enables better modeling of basic hydrology and allows us to examine the effects of rising seas on saltmarshes and other sensitive habitats or species we monitor in Great Bay.


Monitoring a system the size and complexity of Great Bay involves many partnerships. The Great Bay Reserves works closely with the Piscataqua Region Estuaries Partnership, which sponsors additional SWMP-style stations on Great Bay, supports a data portal at the New Hampshire Department of Environmental Services Great Bay website, and coordinates a periodic State of Our Estuaries Report.

Our Reserve participates in regional networks, including the Gulf of Maine Council’s EcoSystem Indicator Partnership (ESIP) and the Northeast Regional Association of Coastal and Ocean Observing Systems (NERACOOS). The University of New Hampshire, a NERACOOS partner, provides additional water quality data at the Great Bay Coastal Buoy website. We are also part of a collaborative monitoring effort for climate change and related stressors let by the Northeast Regional Ocean Council (NROC) and NERACOOS.


We are working with NOAA’s Office for Coastal Managament to develop high resolution coastal wetland habitat maps for New Hampshire. These maps will be complete in 2019 and will form the basis for a new landscape scale assessment of marsh resiliency. They will also help prioritize future field monitoring conducted by the Great Bay Reserve and our partners. These maps will also inform the Piscataqua Region Estuaries Partnership’s work on salt marsh indicators that is part of the “State of Our Estuaries” report and monitoring.

You can view a current habitat map here.