In the upper reaches of estuaries, the pulsing of nutrient inputs and salinity occurs on fine temporal and spatial scales. We investigated the supply and exchanges of N, P, and S along a salinity gradient in a Chesapeake Bay subestuary. Interactions among nutrients in surface water, sediment porewater, and shoots of the dominant marsh macrophyte Spartina alterniflora were also examined. The system was characterized by a spatial gradient in nutrient availability, with the low salinity region representing abundant allochthonous nitrogen and phosphorus inputs and minimal sulfur availability. Autochthonous production and consumption of nutrients were most important at the midpoint of the salinity gradient. These patterns were reflected in the N, P, and S content of S. alterniflora over one growing season. This brackish tidal creek system also had a gradient of temporal variability in levels of inorganic nitrogen, phosphorus, and sulfur. The higher salinity portion experienced the damping effect of waters of more constant nutrient composition, whereas the upper portion of the system was characterized by highly pulsed nutrient availability. Interchanges between nutrient pools were apparent throughout the system. Sediment, and even surface-water, concentrations of nutrients seemed to respond to plant root zone oxidation and uptake and release of nutrients. Porewater biogeochemical processes were linked to surface-water nutrient dynamics as well.