Benthic foraminifera influenced by the Mississippi River plume and seasonal hypoxia were assessed from Louisiana inner-continental shelf sediment samples. Surface foraminifera assemblages were representative of in-situ populations as established by staining techniques. Community diversity and richness/evenness analyses indicate three regimes: high stress (sediment dominated), intermediate stress (hypoxia dominated), and low stress (low sediment accumulation/high oxygen). Epistominella vitrea and Buliminella morgani are useful tracers of rapid sediment accumulation rate and hypoxia. A bottom-water productivity signal west of the Mississippi River plume is indicated by benthic and planktic foraminifera abundance peaks. Surface benthic foraminifera trends are utilized to interpret changes in historical community structure from hypoxic-area sediments deposited since the turn of the century. The hypoxia-tolerant species Buliminella morgani increases markedly upcore, while hypoxia intolerant species decrease or disappear. Diversity and dominance trends temporally correspond to a dramatic increase in U.S. fertilizer application. The results of this study have application to paleoenvironmental research spanning longer geologic timescales. The documented relationships between population structure and stressors in river-dominated marine systems may provide a useful analog for recognition of these conditions in the fossil record.