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.