As the river mixes with the salty water of Pamlico Sound, settling, assimilation, and dilution with nitrogen-poor seawater cause reduced nitrogen levels in the Pamlico River tributaries of Van Swamp, Pungo River, and Durham, Pungo, and Pantego Creeks. Total phosphorus values are generally highest in the mainstream Pamlico River from Tarboro to the Pamlico Sound. The highest mean concentrations of phosphorus are found just downstream of PCS Phosphate in Beaufort County. Water quality in the estuarine part of the basin is poor where waters are impacted by algal blooms and bacterial contamination. All waters from Bath Creek to Washington are impaired.
Fish kills, fish diseases, and low oxygen levels are chronic problems.
Low dissolved oxygen concentrations attributed to algal blooms have occurred predominately in the waters between Washington and Bath. Persistent problems occur in Blounts Creek, Bath Creek, Pungo Creek near Belhaven, and in the tributaries near Campbell and Eastham Creeks. There are 128 permitted surface water dischargers to both fresh and salt water in the basin. The majority of these dischargers are municipal wastewater treatment plants located in the headwater counties of Granville, Franklin, and Nash. Seven dischargers in the Tar-Pamlico basin have toxics loadings that exceed 1,000 pounds per year.