The Estuary Program is a member of the National Estuary Program (NEP) of the EPA. The program is made up of 28 estuary programs throughout the country that protect and restore estuaries of national significance. The NEP is a voluntary, placed-based program established by Congress and authorized by Section 320 of the Clean Water Act in 1987.

The Association of National Estuary Programs (ANEP) is a nonprofit organization dedicated to supporting and connecting the 28 NEPs. They work to educate stakeholders and elected officials on the value of estuaries and water quality to coastal communities.