Dissolved inorganic nitrogen (DIN) retention-transport through a headwater catchment was synthesized from studies encompassing four distinct hydrologic zones of the Shingobee River Headwaters near the origin of the Mississippi River. The hydrologic zones included: (1) hillslope ground water (ridge to bankside riparian); (2) alluvial riparian ground water; (3) ground water discharged through subchannel sediments (hyporheic zone); and (4) channel surface water. During subsurface hillslope transport through Zone 1, DIN, primarily nitrate, decreased from ∼3 mg-N/l to <0.1 mg-N/l. Ambient seasonal nitrate:chloride ratios in hillslope flow paths indicated both dilution and biotic processing caused nitrate loss. Biologically available organic carbon controlled biotic nitrate retention during hillslope transport. In the alluvial riparian zone (Zone 2) biologically available organic carbon controlled nitrate depletion although processing of both ambient and amended nitrate was faster during the summer than winter. In the hyporheic zone (Zone 3) and stream surface water (Zone 4) DIN retention was primarily controlled by temperature. Perfusion core studies using hyporheic sediment indicated sufficient organic carbon in bed sediments to retain ground water DIN via coupled nitrification-denitrification. Numerical simulations of seasonal hyporheic sediment nitrification-denitrification rates from perfusion cores adequately predicted surface water ammonium but not nitrate when compared to 5 years of monthly field data (1989-93). Mass balance studies in stream surface water indicated proportionally higher summer than winter N retention. Watershed DIN retention was effective during summer under the current land use of intermittently grazed pasture. However, more intensive land use such as row crop agriculture would decrease nitrate retention efficiency and increase loads to surface water. Understanding DIN retention capacity throughout the system, including special channel features such as sloughs, wetlands and floodplains that provide surface water-ground water connectivity, will be required to develop effective nitrate management strategies.