We measured benthic and water column fluxes in a hypersaline coastal system (Baffin Bay, Texas) in 1996-1997, a period of decreasing salinity (increased freshwater input) and turbidity. Salinity decreased from a mean of 60 to 32 practical salinity units (psu) and turbidity decreased from a mean of 78 to 25 NTU over the study period. Associated with hydrological changes, there were important changes in nutrient fluxes and metabolism. There was a shift of total respiration from the water column to the sediments and an increased amount of the benthic metabolism (2-67%) was attributed to sulfate reduction in this system when salinity was lowest, perhaps a consequence of increased benthic light levels and photosynthetic production of labile carbon in the sediments. The sediments were a large sink for both N and P. Sediment particulate C:N (9.8) and C:P (119) ratios were lower than those in the water column. However, ammonium:phosphate fluxes increased coincident with increased sulfate reduction rates and porewater sulfide concentrations. Efficient N-retention mediated through dissimilative nitrate reduction to ammonium, and high rates of N-fixation in shallow, hypersaline systems may facilitate transitions from N-limitation to P-limitation. During the most hypersaline period, seston exhibited some of the most extreme nutrient ratios ever reported for a marine ecosystem (C:N 10-37 and C:P 200-1200) and suggest that plankton are likely to be P-limited or are very well adapted to low P availability. When salinity and N:P and C:P ratios were highest, the plankton was dominated by a brown tide alga ( Aureoumbra lagunensis), supporting evidence that this organism is adapted to low P, long residence time systems.