The discharge of excess nitrogen to streams and rivers poses an existential threat to both humans and ecosystems. A seminal study of headwater streams across the United States concluded that in-stream removal of nitrate is controlled primarily by stream chemistry and biology. Reanalysis of these data reveals that stream turbulence (in particular, turbulent mass transfer across the concentration boundary layer) imposes a previously unrecognized upper limit on the rate at which nitrate is removed from streams. The upper limit closely approximates measured nitrate removal rates in streams with low concentrations of this pollutant, a discovery that should inform stream restoration designs and efforts to assess the effects of nitrogen pollution on receiving water quality and the global nitrogen cycle.

Modeling and experimental studies demonstrate that ambient groundwater reduces hyporheic exchange, but the implications of this observation for stream N‐cycling is not yet clear. Here we utilize a simple process‐based model (the Pumping and Streamline Segregation or PASS model) to evaluate N‐cycling over two scales of hyporheic exchange (fluvial ripples and riffle‐pool sequences), ten ambient groundwater and stream flow scenarios (five gaining and losing conditions and two stream discharges), and three biogeochemical settings (identified based on a principal component analysis of previously published measurements in streams throughout the United States). Model‐data comparisons indicate that our model provides realistic estimates for direct denitrification of stream nitrate, but overpredicts nitrification and coupled nitrification‐denitrification. Riffle‐pool sequences are responsible for most of the N‐processing, despite the fact that fluvial ripples generate 3–11 times more hyporheic exchange flux. Across all scenarios, hyporheic exchange flux and the Damköhler Number emerge as primary controls on stream N‐cycling; the former regulates trafficking of nutrients and oxygen across the sediment‐water interface, while the latter quantifies the relative rates of organic carbon mineralization and advective transport in streambed sediments. Vertical groundwater flux modulates both of these master variables in ways that tend to diminish stream N‐cycling. Thus, anthropogenic perturbations of ambient groundwater flows (e.g., by urbanization, agricultural activities, groundwater mining, and/or climate change) may compromise some of the key ecosystem services provided by streams.

A simple analytical model is presented for the removal of stream-borne contaminants by hyporheic exchange across duned or rippled streambeds. The model assumes a steady-state balance between contaminant supply from the stream and first-order reaction in the sediment. Hyporheic exchange occurs by bed form pumping, in which water and contaminants flow into bed forms in highpressure regions (downwelling zones) and out of bed forms in low-pressure regions (upwelling zones). Model-predicted contaminant concentrations are higher in downwelling zones than upwelling zones, reflecting the strong coupling that exists between transport and reaction in these systems. When flow-averaged, the concentration difference across upwelling and downwelling zones drives a net contaminant flux into the sediment bed proportional to the average downwelling velocity. The downwelling velocity is functionally equivalent to a mass transfer coefficient, and can be estimated from stream state variables including stream velocity, bed form geometry, and the hydraulic conductivity and porosity of the sediment. Increasing the mass transfer coefficient increases the fraction of streamwater cycling through the hyporheic zone (per unit length of stream) but also decreases the time contaminants undergo first-order reaction in the sediment. As a consequence, small changes in stream state variables can significantly alter the performance of hyporheic zone treatment systems.