The National Estuarine Research Reserve System is a network of 30 protected areas established by partnerships between the National Oceanic and Atmospheric Administration (NOAA) and coastal states. The reserves represent different biogeographic regions of the United States. The National Estuarine Research Reserve System protects more than 1.3 million acres of coastal and estuarine habitats for long-term research, water-quality monitoring, education, and coastal stewardship.

For thousands of years, coastal and estuarine environments have provided people with food, safe harbors, transportation access, flood control, and a place to play and relax. The pressures on the nation's coast are enormous and the impacts on economies and ecosystems are becoming increasingly evident. Severe storms, climate change, pollution, habitat alteration and rapid population growth threaten the ecological functions that have supported coastal communities throughout history. Estuaries are the connection between the ocean (or Great Lakes) and the land and humans depend on both for their very existence, so caring for both – and the connection between them – is vital to humans.

The System was established by the Coastal Zone Management Act (CZMA) of 1972 as estuarine sanctuaries and was renamed to estuarine research reserves in the 1988 reauthorization of the CZMA. NOAA provides funding, national guidance and technical assistance. Each reserve is managed on daily basis by a lead state agency or university, with input from local partners.

Reserve staff work with local communities and regional groups to address natural resource management issues, such as non-point source pollution, habitat restoration and invasive species. Through integrated research and education, the reserves help communities develop strategies to deal successfully with these coastal resource issues. Reserves provide adult audiences with training on estuarine issues of concern in their local communities, offer field classes for K-12 students, and provide estuary education to teachers through the Teachers on the Estuary program. Reserves also provide long-term water quality monitoring as well as opportunities for both scientists and graduate students to conduct research in a "living laboratory".

The National Estuarine Research Reserves serve as living laboratories to support coastal research and long-term monitoring and to provide facilities for on-site staff, visiting scientists and graduate students. They also serve as reference sites for comparative studies on coastal topics such as ecosystem dynamics, human influences on estuarine systems, habitat conservation and restoration, species management, and social science. Additionally, the reserves serve as sentinel sites to better understand the effects of climate change.

The goals of the Reserve System's research and monitoring program include:

Each reserve works on a variety of research projects, in addition to participating in the System-wide Monitoring Program. The topics of these projects are varied and depend on local needs and issues, as well as issues of national concern. Topics may include issues such as investigating the impacts of non-point source pollution, understanding the role of social science in coastal resource management, and controlling invasive species.

The System Wide Monitoring Program (SWMP, pronounced "swamp") was established in 1995 as a means of observing short-term variability and long-term changes in estuarine regions. Each reserve participates in SWMP which provides researchers, resource managers, educators, and other coastal decision makers with standardized, quantitative measures to determine how reserve conditions are changing. By using standard operating procedures for each component across all 30 reserves, SWMP data helps establish the reserves as a system of national reference sites, as well a network of sentinel sites for detecting and understanding the effects of climate change in coastal regions.