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 of the ability of the water to support human uses.
Nutrient levels are of specific 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.