Bi-weekly water sampling and in situ measurements were performed at fixed sampling stations. In situ measurements were performed throughout the water column in 0.5 meter depth increments. Parameters measured include: temperature, salinity, specific conductivity, dissolved oxygen (DO), pH, chlorophyll fluorescence, photosynthetically active radiation (PAR), turbidity, and barometric pressure.

Methods
Water sampling was conducted bi-weekly. When collection was split over two days, a single date was used based on the upstream or majority stations.

Stations were selected to cover the entire length of the Neuse River Estuary from Streets Ferry Bridge (Station 0) to the mouth of the estuary where it flows into Pamlico Sound. When possible, efforts were made to select locations with key stationary features (channel markers, buoys and land markers) to allow easy station identification in the field.

Surface water samples were collected by submerging 10 liter high-density polyethylene containers just below the water surface or by filling the containers with surface water collected from bucket casts. Bottom water samples were collected with a horizontal plastic Van Dorn sampler. Starting December 2007, all samples collected with diaphragm pump and a weighted, marked hose. All containers were kept in dark coolers at ambient temperature during transport to the laboratory. All filtration was done within a few hours of collection and when conditions permitted, on board the research vessel.

Prior to the 09/13/2000 sampling date, in situ measurements were performed at discrete depths using a Hydrolab Data Sonde 3 equipped with a multiprobe and SVR3 display logger. Beginning on the 09/13/2000 sampling date, in situ measurements were performed at discrete depths on the sunlit side of the research vessel using a Yellow Springs Instruments (YSI Incoporated, Ohio) multiparameter sonde (Model 6600 or 6600 EDS-S Extended Deployment System) equipped with a YSI conductivity/temperature probe (Model 6560), a YSI chlorophyll probe (Model 6025), a YSI pH probe (Model 6561 or 6566), a YSI pulsed dissolved oxygen probe (Model 6562), a self cleaning YSI turbidity probe (Model 6026 or 6136), and beginning on the 07/30/2003 sampling date, a flat Li-Cor sensor (UWQ-PAR 6067). The YSI sonde was coupled to a either a YSI 610 DM datalogger or a YSI 650 MDS Multi-parameter Display System datalogger. In situ measurements were performed at the surface (approximately 0.2 meters) and at the bottom of the water column (approximately 0.5 meters from the sediment layer). These data are included in the worksheet titled "NRE Dataset." In situ measurements were also performed throughout the water column in 0.5 meter depth increments. These data are included in the worksheet titled "NRE YSI Profiles." The data were stored on the datalogger and downloaded to Ecowin software upon return to the laboratory.

Distance (in river kilometers) was calculated using ESRI ArcGIS software. Distances were calculated using projected station locations (North Carolina State Plane 1983 meters projection). Distances from station 0 through 30 (upper river stations) were measured along the main channel of the river. Distances from stations 30 to 180 were measured as straight lines between stations