NERRS System-wide monitoring program

Characteristics of Land Use & Ecosystems

Characteristics of Land Use and Ecosystems (CLUE)is a multidimensional matrix that puts data from the NERRS System-Wide Monitoring Program (SWMP)  in the context of surrounding ecosystems and watersheds. Reserves maintain more than 280 stations that collect water quality data to support research, education, public health, resource management, resilience planning, and disaster recovery. With CLUE, scientists, educators, and others can explore a range of influences on this data—at one Reserve and across the national System. CLUE was developed with funding from NOAA’s Office for Coastal Management.



Jude Apple
Padilla Bay Reserve

Erik Smith
North Inlet-Winyah Bay Reserve


Building CLUE

Land use, habitats and plants, estuary type, geologic setting—there are many factors that influence coastal water quality. For example, impervious surfaces and agriculture can contribute to nutrient pollution and decreased levels of dissolved oxygen, while natural ecosystems such as saltmarshes and eelgrass meadows can reduce turbidity and increase oxygen in surface waters.  Understanding the relationship between changing land use, water quality, and ecosystem health is at the core of the SWMP station network. 

To help users of NERR water quality monitoring data better understand the physical and ecological attributes of the lands and waters that surround SWMP WQ stations, the NERRS team adapted two commonly used classification systems: the Coastal Change Analysis Program’s (C-CAP) and Coastal and Marine Ecological Classification Standard (CMECS). C-CAP is a nationally standardized inventory of land cover for coastal areas, and CMECS is a federal standard for interpreting and classifying observational data about coastal and marine environments.

Chosen to reflect the geographic and biological diversity of estuaries through the U.S. Coastal Zone, each of the 29 NERR sites manages a standardized water quality monitoring program.

Combining CMECS, C-CAP & SWMP

Using C-CAP, the team determined land cover for the watersheds of each station. They then adjusted parameters from CMECS to include freshwater and riverine systems, resulting in 48 unique descriptors for the physical characteristics of these ecosystems. There is more room here an below to add more detail about development that you think is important to highlight.


This new, nationally standardized classification system allows users of SWMP data to better understand the following characteristics of the ecosystems and watersheds surrounding stations:

Biogeographic Setting

Aquatic Setting

Water Column Component

Geoform Component

Land Cover

Substrate Component

Biotic Setting

Exploring Patterns in the NERRS

The CLUE dashboard or map allows one to explore the connections between habitats, land uses, salinity regimes, and more for SWMP stations at individual Reserves and at different scales in the NERRS. Such analyses can reveal patterns in ecosystem features, land cover, and water quality data within the NERRS.

What are the most common habitats monitored by SWMP?

79% of SWMP stations are located in emergent tidal marshes, SAV beds, or open water. 

Putting CLUE to Work

CLUE allows scientists, resource managers, and educators to place a decades-in-the-making national dataset on water quality  in the context for shifting coastal conditions.


the CLUE can facilitate basic estuarine science, as well as research to address coastal community needs. The Classification Matrix (link) characterizes all of NERRS SWMP monitoring sites sites. It allows users to code, sort, and filter data to support research that depends on data from an individual SWMP station, cross-Reserve analyses, and large-scale syntheses and hypothesis driven questions about the response of estuaries to change. It also provides collaborative opportunities for researchers interested in studying specific ecological settings. CLUE can be adapted to advance classification for other monitoring stations.


CLUE can inform how land or habitat cover changes impact water quality changes can inform land use decisions. Citizen water quality monitoring networks can use station information to identify monitoring locations in the watershed. This inventory of habitats, landscapes, and estuary types also can support strategic decisions about new Reserves, beyond the biogeographic or state level.

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CLUE is an important addition to NERRS andNOAA resources designed to help educators bring estuarine science into the classroom through hands-on experiments, fieldwork, and data explorations. These experiences provide an exciting entry for people to become actively involved in coastal conservation.

CLUE can enhance Teachers on the Estuary (TOTE) activities to explore questions like:

—What’s the diversity of habitats in our estuary? Where else should we look for these habitats.

—How many Reserves have eelgrass to support the critters we’re learning about?

The CLUE dashboard can be used to create virtual and off-site field trips for students who can’t visit the Reserve in person—whether it’s in their state or across the country!