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.

Estimates of streambed water flux are needed for the interpretation of streambed chemistry and reactions. Continuous temperature and head monitoring in stream reaches within four agricultural watersheds (Leary Weber Ditch, IN; Maple Creek, NE; DR2 Drain, WA; and Merced River, CA) allowed heat to be used as a tracer to study the temporal and spatial variability of fluxes through the streambed. Synoptic methods (seepage meter and differential discharge measurements) were compared with estimates obtained by using heat as a tracer. Water flux was estimated by modeling one‐dimensional vertical flow of water and heat using the model VS2DH. Flux was influenced by physical heterogeneity of the stream channel and temporal variability in stream and ground‐water levels. During most of the study period (April–December 2004), flux was upward through the streambeds. At the IN, NE, and CA sites, high‐stage events resulted in rapid reversal of flow direction inducing short‐term surface‐water flow into the streambed. During late summer at the IN site, regional ground‐water levels dropped, leading to surface‐water loss to ground water that resulted in drying of the ditch. Synoptic measurements of flux generally supported the model flux estimates. Water flow through the streambed was roughly an order of magnitude larger in the humid basins (IN and NE) than in the arid basins (WA and CA). Downward flux, in response to sudden high streamflows, and seasonal variability in flux was most pronounced in the humid basins and in high conductivity zones in the streambed.

Graphs showing VS2DH modeling results for the Newman site, including simulated temperatures, measures of bias, and associated root mean-square error for observed temperatures at 0.5 foot below the streambed, 1.0 foot below the streambed, 1.5 feet below the streambed, and 3.0 feet below the streambed ..........44 33. Graphs showing VS2DH modeling results for the Crows Landing site, including simulated temperatures, measures of bias, and associated root mean-square error for observed temperatures at 0.5 foot below the streambed, 1.0 feet below the streambed, 1.5 feet below the streambed, and 3.0 feet below the streambed ................45 34. Graphs showing VS2DH modeling results for the Vernalis site, including simulated temperatures, measures of bias, and associated root mean-square error for observed temperatures at 0.5 foot below the streambed, 1.0 feet below the streambed, 1.5 feet below the streambed, and 3.

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