Physical, chemical, hydrologic, and biologic factors affecting nitrate (NO3(-)) removal were evaluated in three agricultural streams draining orchard/dairy and row crop settings. Using 3-d "snapshots" during biotically active periods, we estimated reach-level NO3(-) sources, NO3(-) mass balance, in-stream processing (nitrification, denitrification, and NO3(-) uptake), and NO3(-) retention potential associated with surface water transport and ground water discharge. Ground water contributed 5 to 11% to stream discharge along the study reaches and 8 to 42% of gross NO3(-) input. Streambed processes potentially reduced 45 to 75% of ground water NO3(-) before discharge to surface water. In all streams, transient storage was of little importance for surface water NO3(-) retention. Estimated nitrification (1.6-4.4 mg N m(-2) h(-1)) and unamended denitrification rates (2.0-16.3 mg N m(-2) h(-1)) in sediment slurries were high relative to pristine streams. Denitrification of NO3(-) was largely independent of nitrification because both stream and ground water were sources of NO3(-). Unamended denitrification rates extrapolated to the reach-scale accounted for <5% of NO3(-) exported from the reaches minimally reducing downstream loads. Nitrate retention as a percentage of gross NO3(-) inputs was >30% in an organic-poor, autotrophic stream with the lowest denitrification potentials and highest benthic chlorophyll a, photosynthesis/respiration ratio, pH, dissolved oxygen, and diurnal NO3(-) variation. Biotic processing potentially removed 75% of ground water NO3(-) at this site, suggesting an important role for photosynthetic assimilation of ground water NO3(-) relative to subsurface denitrification as water passed directly through benthic diatom beds.