Restore, maintain or enhance water quality in the Albemarle-Pamlico region so that it is fit for fish, wildlife and recreation.
The primary water quality concern in the Albemarle-Pamlico region is the inability of 42 percent of the freshwater miles and 8 percent of the saltwater acres to fully support their designated uses. An additional 32 percent of the freshwater miles and 4percent of the saltwater acres are threatened in their ability to continue to support their uses.
Much of the impairment of waters in the APES system can be attributed to nonpoint sources of pollution. The most prominent of these sources has been agricultural runoff, but runoff from construction, forestry, urban runoff, waste disposal 
areas, and airborne pollutants also make significant contributions to the impairment of APES region waters.
A smaller, but still significant amount of water quality impairment in the region can be attributed to point source dischargers. These sources of pollution contribute to the elevation of sediment, nutrients, biological oxygen demand, toxicants and fecal coliform in the water. These factors all cause degradation of habitat for living marine organisms and harm the ability of the water to support human uses.
Nutrient levels are a concern in several APES region river basins. The impacts of toxicants and bacteria have been shown to cause localized water quality problems across the APES system.
The importance of a systemwide strategy in effective resource management has been emphasized in the Comprehensive Conservation and Management Plan.
- Objective A Implement a comprehensive basinwide approach to water quality management.
- Objective B
Reduce sediments, nutrients and toxicants from nonpoint sources. - Objective C
Reduce pollution from point sources, such as wastewater treatment facilities and industry. - Objective D
Reduce the risk of toxic contamination to aquatic life and human health. - Objective E
Evaluate indicators of environmental stress in the estuary and develop new techniques to better assess water quality degradation.