Water quality in the basin has been a concern for over a century.  High nitrogen levels from wastewater discharges, urban stormwater, and agricultural runoff have caused frequent algal blooms, hypoxic conditions, and fish kills.  In 1997 the North Carolina Environmental Management Commission (EMC) adopted the state’s first mandatory plan to control both point and nonpoint source pollution in the basin. The plan, backed by figures in the Neuse River Total Maximum Daily Load (TMDL), called for a mandatory 30 percent reduction in nitrogen from both urban and rural sources by 2003.  The North Carolina Division of Water Quality worked with the appropriate agricultural agencies to enroll croplands in nutrient reduction conservation programs.  Between 1996 and 2003, it was estimated that half of the croplands enrolled in the program implemented BMPs.  

Through 2002 more than $12 million was committed to meeting project goals. The section 319 program provided approximately $3.8 million in project funds, with more than $1 million contributing directly to the installation of BMPs on farms. Additional project funding was provided by the NRCS Environmental Quality Incentives Program ($4.7 million), North Carolina Agriculture Cost Share Program ($3.2 million), Clean Water Management Trust Fund ($2.7 million), and Pew Charitable Trust.