Seasonally severe hypoxia (less than or equal to 2 mg O-2 1(-1)) occurs in waters below the pycnocline on the northern Gulf of Mexico inner continental shelf in May through September over extensive areas (up to 18000 km(2)). Spatial and temporal variability in the distribution of hypoxic water masses is related, in part, to the amplitude and phasing of freshwater discharge from the Mississippi and Atchafalaya Rivers, circulation patterns, nutrient flux and a close coupling with net productivity. The Mississippi River flood in 1993 and sustained freshwater inputs to the Gulf of Mexico occurred during mid-summer through early autumn when long-term mean flows (1930-1995) are normally lowest. Long-term studies of the Louisiana shelf hypoxic zone provided a natural experiment to examine the effects of extreme high river flow on the adjacent continental shelf. Oxygen levels in bottom waters were severely reduced in July, August and September compared to long-term averages (1985-1992). Also, the areal extent of the bottom-water hypoxia in mid-summer 1993 was approximately twice as large as the average area mapped in the previous 8 years during mid-summer shelfwide surveys. Contributing to increased severity and areal extent of hypoxia in 1993 were reduced surface water salinities, increased strength of the pycnocline, five to ten times higher nutrient concentrations, greater phytoplankton biomass, an order of magnitude greater abundance of phytoplankton, mostly small, coccoid cyanobacteria, and a shift in diatom community dynamics. An equally extensive hypoxic zone in mid-summer of 1994, when riverine fluxes of freshwater and nutrients were 'normal', suggests some residual effects of the 1993 summer flooding. (C) 1998 John Wiley & Sons, Ltd.