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Sediment-water nutrient and oxygen exchanges were measured under light and dark conditions at 1 oligohaline (Stn D) and 1 mesohaline (Stn A) shallow (1 m) site in the Neuse River estuary, North Carolina. USA. Mean respiration rates were very similar between sites (11 to 12 mg 0 2 m-' h-'), but maximum net productivity at the mesohaline site (74 mg Oz m-' h-') was nearly twice that of the oligohaline site (40 mg O2 m-2 h-'). NH4 fluxes were also significantly different. On average, releases of NH, from sediments at both sites occurred in the dark (13 to 22 pm01 N h-' for Stns D and A, respectively) and, slightly, at the lowest irradiance (67 E m-' S-'. 0.3 to 5 pm01 N h-'). NH, was taken up at average rates between 3 and 12 pm01 N m-' h-' at 3 higher irradiances. Mean NO, (nitrate + nitnte) fluxes were very low ( < l 0 pm01 N m-2 h-'), nearly always directed out of the sediment, and not significantly different. Filterable reactive phosphorus fluxes also did not follow any consistent response to changes in irradiance. Flux vs irradiance curves were used in conjunction with estimates of in situ light availability to the benthos to compute ecosystem-level influence of autotrophy on material exchanges. The autotropic-heterotrophic transitions were 1 to 2 m (oligohaline) and 3 to 4 m (mesohaline). When integrated over depth and area the mesohaline sediments were always net NH, sources to the water column, net O2 sources in fall and winter and net O2 sinks in spring and summer. Oligohaline sediments were O2 sinks except during fall, and NH, sources only in winter and summer. Cultural eutrophication has the potential to alter the balance of benthic autotrophy and heterotrophy which in turn may foster phytoplanktonic productivity.