Although numerous studies of hyporheic exchange and denitrification have been conducted in pristine, high-gradient streams, few studies of this type have been conducted in nutrient-rich, low-gradient streams. This is a particularly important subject given the interest in nitrogen (N) inputs to the Gulf of Mexico and other eutrophic aquatic systems. A combination of hydrologic, mineralogical, chemical, dissolved gas, and isotopic data were used to determine the processes controlling transport and fate of NO₃ ⁻ in streambeds at five sites across the USA. Water samples were collected from streambeds at depths ranging from 0.3 to 3 m at three to five points across the stream and in two to five separate transects. Residence times of water ranging from 0.28 to 34.7 d m⁻¹ in the streambeds of N-rich watersheds played an important role in allowing denitrification to decrease NO₃ ⁻ concentrations. Where potential electron donors were limited and residence times were short, denitrification was limited. Consequently, in spite of reducing conditions at some sites, NO₃ ⁻ was transported into the stream. At two of the five study sites, NO₃ ⁻ in surface water infiltrated the streambeds and concentrations decreased, supporting current models that NO₃ ⁻ would be retained in N-rich streams. At the other three study sites, hydrogeologic controls limited or prevented infiltration of surface water into the streambed, and ground-water discharge contributed to NO₃ ⁻ loads. Our results also show that in these low hydrologic-gradient systems, storm and other high-flow events can be important factors for increasing surface-water movement into streambeds.