To delay enforcement and establishment of certain water quality standards within the Great Bay Estuary, and for other purposes.

Prohibits the Administrator of the Environmental Protection Agency (EPA), for five years, from: (1) requiring a publicly owned treatment works that contributes nitrogen loadings to the Great Bay Estuary to commence construction on any upgrade of a facility for the purpose of enforcing water quality standards or effluent limitations with regard to nitrogen under the Federal Water Pollution Control Act (commonly known as the Clean Water Act); or (2) establishing any water quality standard or effluent limitation with regard to nitrogen in the such Estuary under such Act.

Requires the Administrator to study eelgrass levels, and the causes of any loss of eelgrass habitat, in such Estuary.

Defines "Great Bay Estuary" to mean the estuarine zone that extends from the mouth of Portsmouth Harbor, in the vicinity of Portsmouth, New Hampshire, to the head-of-tide for the eight rivers (including the tributaries of those rivers) that flow into Great Bay, Little Bay, and the Piscataqua River.