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Large-scale hypoxia regularly develops during the summer on the Louisiana continental shelf. Traditionally, hypoxia has been linked to the vast winter and spring nutrient inputs from the Mississippi River and its distributary, the Atchafalaya River. However, recent studies indicate that much of the shelf ecosystem is heterotrophic. We used data from five late July shelfwide cruises from 2006 to 2010 to examine carbon and oxygen production and identify net autotrophic areas of phytoplankton growth on the Louisiana shelf. During these summer times of moderate river flows, shelfwide pH and particulate organic carbon (POC) consistently showed strong signals for net autotrophy in low salinity (<25) waters near the river mouths. There was substantial POC removal via grazing and sedimentation in near-river regions, with 66–85 % of POC lost from surface waters in the low and mid-salinity ranges without producing strong respiration signals in surface waters. This POC removal in nearshore environments indicates highly efficient algal retention by the shelf ecosystem. Updated carbon export calculations for local estuaries and a preliminary shelfwide carbon budget agree with older concepts that offshore hypoxia is linked strongly to nutrient loading from the Mississippi River, but a new emphasis on cross-shelf dynamics emerged in this research. Cross-shelf transects indicated that river-influenced nearshore waters <15 m deep are strong sources of net carbon production, with currents and wave-induced resuspension likely transporting this POC offshore to fuel hypoxia in adjacent mid-shelf bottom waters.