The Long Island Sound Study (LISS) works with federal, state, and local partners to restore and protect Long Island Sound. In 1994, the program’s goals were identified in LISS’s Comprehensive Conservation and Management Plan (the CCMP).

The Indian River Lagoon National Estuary Program is a partnership whose members work to improve the water quality and ecological integrity of the 156-mile-long estuary on Florida’s east coast. The U.S. Environmental Protection Agency (EPA) designated the lagoon as “an estuary of national significance” in April 1990 and included the lagoon in the National Estuary Program. The St. Johns River and South Florida water management districts, the five counties that border the lagoon — Brevard, Indian River, Martin, St.

The National Estuary Program (NEP) was established by Section 320 of the Water Quality Act of 1987. Section 320 authorizes the Administrator of the U.S. Environmental Protection Agency (EPA) to convene Management Conferences to develop Comprehensive Conservation and Management Plans (CCMPs) for estuaries of national significance that are threatened by pollution, development or overuse. Section 320 also outlines the estuary designation process and the purposes of the Management Conference.

The Casco Bay Estuary Partnership (CBEP) is one of 28 National Estuary Programs under the U.S. Environmental Protection Agency. It is a collaborative effort of local, state, and federal government organizations, non-profits, local businesses, citizens, and universities dedicated to protecting and restoring Casco Bay, Maine.

The Barnegat Bay Partnership (formerly the Barnegat Bay National Estuary Program) is one of 28 designated National Estuary Programs throughout the United States working to improve the health of nationally significant estuaries. The program is sponsored by the United States Environmental Protection Agency, the Ocean County Board of Chosen Freeholders, and Ocean County College.

The Tampa Bay Estuary Program was created by Congress in 1991 to assist the community in restoring and protecting Florida's largest open-water estuary. As a designated "estuary of national significance," Tampa Bay is the economic and environmental centerpiece of a rapidly growing region supporting more than 2.3 million people.

The San Francisco Estuary Partnership is a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary.

Beginning in 1995, the New Hampshire Estuaries Project (NHEP) embarked on a process to develop and systematically address the 98 Action Items outlined in the program's guiding document, the Comprehensive Conservation and Management Plan.