High resolution sampling surveys in the York River estuary (YRE): performed in 2018 during Feb, March, June, August, and October and in 2019 during Feb, April, July, and October at dawn, dusk, and the following dawn along a zig-zag cruise track, covering approximately equal areas of shoal and channel, a total distance of 30 km, using a DataFlow system modified from Madden and Day (1992). All sampling is performed during spring tides, the period following de-stratification in the YRE when the system is well-mixed (Haas 1977). This high resolution sampling plan enables us to capture day-time primary production (dawn to dusk) and night-time respiration (dusk to dawn) while sampling water masses exposed to the same tidal stage. The DataFlow system captures continuous measurements of water quality parameters and allows grab sampling (at five channel and five shoal stations) for DIC and other parameters shown in different spread sheets and used for multiple regression analyses. The pCO₂-DataFlow system is instrumented with a pCO₂ analyzer, a multi-parameter datasonde (YSI 6600V2), Wet Labs CDOM sensor, Garmin global positioning system (GPS MAP 546S), and data acquisition system. The system continuously samples surface water (approximately every 30 m at an average speed of 20 knots) from a stern-mounted water intake located 0.5 m below the water surface with a pump, which delivers water in parallel to (1) a shower-head equilibrator and (2) a flow-through cell attached to the YSI which is configured to measure water temperature, salinity, chl-a fluorescence, DO, pH, and turbidity. pCO₂ in the equilibration chamber is determined by recirculating a carrier gas at a flow of approximately 1.5 L min⁻¹ through the equilibrator chamber and a nondispersive infrared absorbance detection analyzer (LI-COR, LI-840). The mole fraction of CO₂ (xCO₂) is corrected for headspace pressure and temperature to determine surface-water pCO₂ with an attainable accuracy of ±4 µatm over the functional range of 100 to 5,000 ppmv (Crosswell et al. 2012). All measurements are taken at 2-second intervals, and the lag time between DataFlow and LI-COR data is measured and corrected for each sampling run. At the beginning, during, and end of each survey, ambient atmospheric air and two CO₂ gas standards (Praxair Inc.) are measured for calibration and verification of the absorbance detection analyzer.

Calculation of Air-Water CO2 and O2 Fluxes: Data in these spreadsheets are used to calculate CO2, O2 fluxes and metabolic parameters as described below. Air-water CO2 and O2 exchanges are driven by the differences between the gas concentrations in the surface water and the atmosphere (ΔpCO2, ΔpO2) scaled by the gas solubility, and the rate of exchange is set by the gas-transfer velocity (k, cm h-1). Input data include: K0, the solubility coefficient (K0(CO2): Weiss 1974; K0(O2): Benson and Krause 1984); k600 the gas exchange coefficient; ΔpCO2 and ΔpO2 and ScSST is the Schmidt number at ambient sea-surface temperature and salinity (Wanninkhof 1992). The gas solubility and Schmidt numbers for CO2 and O2 are determined based on temperature and salinity. The transfer velocity k is parameterized as a function of wind speed normalized to 10 m above the water surface (u10). We calculate air-water CO2 fluxes using the Jiang et al. (2008) parameterization, which provides a conservative estimate of k and has been widely used in reviews of estuarine CO2 fluxes (Crosswell et al 2014).

Spatial and Diel Interpolation of Dawn-Dusk Data for Calculation of Daily CO2 and O2 Fluxes: Data from each dawn–dusk survey is spatially averaged by calculating distance-weighted means of ΔpCO2 and delta pO2 (difference water and atmospheric concentrations), water temperature, salinity and other parameters within a series of five boxes of the YRE. Data are used to calculate CO2 and O2 fluxes, and metabolic parameters as described below.

Open Water measurements of metabolism (based on diel variations of DO): NEM gross primary production (GPP), and respiration (R) are determined from changes in DO concentrations in Dataflow samples collected at dawn, dusk, and the following dawn using the open water method (Kemp and Boynton 1980). ∆DO (dawn to dusk; dusk to dawn), corrected for air/sea exchanges of O2 are used to calculate NEM, GPP, and R. To scale metabolic measurements to regional estimates, the surface areas and water volumes of the YRE were determined for each spatial element using ArcGIS 10 and bathymetric data. Daily average hourly O2 fluxes (mmol DO m-2 d-1) for each box are multiplied by their respective spatial element areas and scaled to annual O2 fluxes. Daily fluxes for each spatial element are summed to provide seasonal and annual totals (moles O2 per m2 per y).