A comprehensive carbon budget was constructed to quantify carbon flows through the freshwater‐marine continuum of a temperate, microtidal estuary. We performed coordinated measurements of dissolved inorganic carbon and total organic carbon fluxes to resolve spatial variability between and along the channel and shoals and diel variability across the entire estuary for 2 yr. Net ecosystem metabolism (NEM) was the most significant control on carbon flow within estuary regions. However, metabolic rates were spatially coupled such that counteracting fluxes across the channel‐shoal gradient or along the river‐ocean gradient resulted in system‐wide NEM that was closely in balance (–3.0 ± 3.3 to 1.1 ± 4.4 molC m−2 yr−1). Similarly, large diel and seasonal variability in air–water CO2 fluxes were observed during 72 spatial surveys, but these short‐term variations generally cancelled out when aggregated to annual budget terms. Although atmospheric exchanges were small (–0.2 ± 0.1 to 2.0 ± 0.4 molC m−2 yr−1), they were subject to large errors (± 4 molC m−2 yr−1) if diel variability was neglected. Internal mechanisms that maintained balanced carbon flows were strongly impacted by river discharge and were only apparent by separately quantifying channel and shoal fluxes. Notably, metabolic responses of the shoal to river forcing outweighed the responses of the channel, and the net impact was contrary to prior relationships derived from synthesis of lower‐resolution carbon budgets. Our budget demonstrates that resolution of carbon fluxes at appropriate scales, including channel‐shoal and diel variability, is critical to characterizing ecosystem function and the fate of carbon within the river‐ocean continuum.

Proper management of shallow coastal systems, which are vulnerable to nutrient enrichment, requires knowledge of land use impacts on nutrient discharges. This study quantified base flow nutrient concentrations and yields for 1 yr (May 2001-April 2002) from 14 first-order streams on the Virginia Eastern Shore (VaES) on the Delmarva Peninsula and assessed their relationships with land cover and soil drainage class in their watersheds. Base flow water discharge rates (1.4-31.5 cm yr(-1)) were likely lower than the long-term average due to a severe drought. Seasonal mean nitrate concentrations were higher in winter, while mean dissolved organic carbon and ammonium concentrations were higher in summer. Annual base flow-weighted mean total dissolved nitrogen (TDN) concentrations were positively related to percent (%) agricultural land cover (r(2) = 0.43; p = 0.02) and % very poorly drained soils (r(2) = 0.51; p = 0.009) and negatively related to % forested land cover (r(2) = 0.54; p = 0.005). Patterns of base flow TDN yields were similar to those of concentrations but were also positively related to % developed land cover (r(2) = 0.40; p = 0.03). Agricultural and developed land covers, together with very poorly drained soil, accounted for 91% of the variability of TDN yields (p = 0.0001). Using a multiple regression model, the base flow TDN loading rate to a coastal lagoon on the VaES, a system vulnerable to nutrient enrichment, was estimated to be 28,170 kg N yr(-1).

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The water-sediment interface is a dynamic zone where the benthic and pelagic environments are linked through exchange and recycling of organic matter and nutrients. However, it is often difficult to measure rate processes in this zone. To that end, we designed an experimental apparatus for continuous and homogeneous perfusion of sediment porewater with dissolved conservative (SF 6 , Rhodamine WT dye) and isotopic (H 13 CO 3 − and 15 NH 4 + ) tracers to study nitrogen and carbon cycling by the sediment microbial community of shallow illuminated sediments. The perfusionator consists of a 60-cm ID×60-cm high cylinder that includes a reservoir for porewater at the base of the sediment column. Porewater amended with conservative and stable isotopic tracers was pumped through a mixing reservoir and upward through the overlying sediments. We tested the perfusionator in a laboratory setting, as part of an outdoor mesocosm array, and buried in coastal sediments. Conservative and isotopic tracers demonstrated that the porewater tracers were distributed homogeneously through the sediment column in all settings. The perfusionator was designed to introduce dissolved stable isotope tracers but is capable of delivering any dissolved ionic, organic, or gaseous constituent. We see a potentially wide application of this technique in the aquatic and marine sciences in laboratory and field settings.