Environmental parameters and organic matter analyses (concentration, absorbance, fluorescence) for dissolved and particulate organic matter for the Neuse River Estuary, North Carolina, USA from 20 July 2015-28 July 2016. Samples were collected bi-weekly from July 2015-October 2015 and March 2016-July 2016 and monthly from November 2015-February 2016. The dataset consists of environmental parameters measured (water temperature, salinity, percent dissolved oxygen, turbidity, chlorophyll-a) and calculated (flushing time) as well as organic matter analyses for dissolved and particulate organic matter (concentration, absorbance, fluorescence) from surface (0.2 m below surface) and bottom (0.5 m above bottom) at 11 stations from the furthest extent of saltwater intrusion (Station 0) to the mouth of the estuary (Station 180). Data were collected as part of the Neuse River Estuary Modeling and Monitoring Program (ModMon; http://paerllab.web.unc.edu/projects/modmon/) at the University of North Carolina - Chapel Hill, Institute of Marine Science.