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Monitoring Programs

Research Programs | Monitoring Programs

Monitoring is an essential part of ecosystem science and management. It provides baseline data to help track natural changes, identify new threats, and assess the effectiveness of management programs. The Great Bay NERR supports and manages programs to monitor water quality as well as key habitats and species in the Great Bay Estuary. Many of our monitoring efforts are conducted as part of the System-Wide Monitoring Program (SWMP), through which all National Estuarine Research Reserves implement consistent protocols to track weather, water quality, and certain habitat conditions. The use of standardized approaches to the collection, analysis, and management of data through the SWMP enables the data to be used for a variety of local purposes as well as for regional and national comparisons of estuarine conditions.

Water Quality and Weather

a map of water and weather monitoring stations
Circles are water quality monitoring stations
The triangle is Great Bay NERR's
weather station
Courtesy of GBNERR's Stewardship Program

The Great Bay NERR's water quality monitoring program was initiated

in 1995 as part of the NERRS' System-wide Monitoring Program (SWMP) and operates through a cooperative agreement with the UNH's Jackson Estuarine Laboratory. The first monitoring station was established in the middle of Great Bay, and subsequent stations have been added in the Squamscott, Lamprey, and Oyster rivers. At each station, a multi-parameter datasonde records temperature, depth, salinity, turbidity, pH, and dissolved oxygen every 15 minutes.

Dissolved inorganic nutrients, suspended solids, particulate organic matter, and chlorophyll-a are also measured monthly at each of the four locations. In addition, the same parameters are tracked at frequent intervals over a full lunar cycle at the Lamprey River location.

Further, a weather station provides contextual information to aid the interpretation of the water quality data. The weather station, located in Greenland, NH, 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 that users of the data can track changes in the environmental conditions in Great Bay. Real-time data for all stations can be viewed at All historical and recent data are available from the NERRS Centralized Data Management Office.

Monitoring a system the size and complexity of Great Bay involves many partnerships. The Piscataqua Region Estuaries Partnership (PREP – A National Estuary Program) sponsors additional SWMP-style stations on Great Bay and provides a data portal at the NH Dept. of Environmental Services Great Bay website. Ocean Observing Systems are becoming more prominent through 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. Great Bay NERR is also working in a regional effort to build a collaborative monitoring effort for climate change and related stressors let by the Northeast Regional Ocean Council (NROC) and NERACOOS. The Reserve also has a strong relationship with the Gulf of Maine Council’s EcoSystem Indicator Partnership (ESIP) to promote monitoring and the use of ecosystem indicators to assess and respond to changes in health of our estuaries. For more information on these partnership programs, please use the links provided or contact the Great Bay Research Coordinator.

For additional water quality data on the Estuary, go to the Great Bay Coastal Buoy website.

a map of salt marsh and SAV monitoring stations
Courtesy of GBNERR's Stewardshp Program

Habitat Monitoring

The Great Bay NERR supports and conducts monitoring programs to establish baseline conditions and track changes in vegetated subtidal (seagrass) and intertidal (saltmarsh) habitats in the Great Bay Estuary.

Seagrass beds provide important spawning, nursery, and feeding habitats for a variety of fish, shellfish, waterfowl, and wading birds. For this reason, recent declines in the spatial extent and biomass of seagrass in the Great Bay Estuary are particularly concerning. In 2007, the Reserve worked with Dr. Fred Short at the UNH Jackson Estuarine Lab to assess in situ conditions within a large eelgrass bed in Great Bay. This effort compared monitoring protocols developed by the NERRS with those used worldwide by SeagrassNet. Since establishing this monitoring site, Dr. Short has continued implementing the SeagrassNet protocols to track changes in eelgrass cover and biomass. The Great Bay NERR also works with the Piscataqua Region Estuaries Partnership (PREP – A National Estuary Program) and the NH Dept. of Environmental Services to support and advise on continuing seagrass mapping efforts and pilot work on macroalgae monitoring.

Salt marshes represent a key intertidal habitat for many species. They also may provide early signals of ecological responses to climate change as plant species may shift due to changing precipitation regimes, temperature, nutrients and water levels. In 2010, the Great Bay NERR began collaborating with Dr. David Burdick at the UNH Jackson Estuarine Lab to begin monitoring vegetation communities and physical conditions in three marshes. This monitoring program has completed surveys in 2010, 2011 and 2013 that will enable us to understand how the spatial and temporal dynamics of emergent vegetation is related to physical factors, such as elevation and salinity. These data will also prove valuable for assessing how climate change may affect the physical and biological structure of marshes in the estuary. Nationally, NERRS is building similar efforts for all 28 Reserves to study how change is manifest in different settings and how we might better adapt and manage these changes.

Great Bay National Estuarine Research Reserve
New Hampshire Fish and Game Department