CZM also administers two National Estuary Programs (NEPs), which are funded by Executive Office of Energy and Environmental Affairs (EEA) and the U.S. Environmental Protection Agency (EPA). The principle goals of these NEPs are to:

• Determine the sources of contaminants that have degraded water quality within these estuaries.
• Develop management recommendations to protect and improve water quality and the health of these estuaries.

The two NEP's in Massachusetts are:

• Buzzards Bay National Estuary Program (formerly the Buzzards Bay Project)
• Massachusetts Bays Program