Agricultural land use alters nitrate (NO₃^–) uptake dynamics in streams, but the specific mechanisms linking individual agricultural stressors to benthic and hyporheic uptake remain unclear. Using stream-side mesocosms and ¹⁵N-nitrate additions, we examined the individual and combined effects of fine sediment (FS) and augmented light and phosphorus levels (L&P) on benthic and hyporheic NO₃^– uptake rates. In absence of FS, L&P stimulated uptake of autotrophic and heterotrophic biofilms, leading to a 12- and 7-fold increase in the benthic and hyporheic compartments, respectively. Under ambient light and nutrient conditions, FS reduced by 3-fold benthic uptake, but effects were not significant. Conversely, in the hyporheic compartment, FS induced anoxic conditions, likely stimulating denitrification and causing a 14-fold increase in hyporheic uptake. When these stressors were combined, they did not interact in the benthic compartment. Conversely, in the hyporheic compartment they interacted antagonistically, with L&P diminishing the increase in uptake induced by FS. Our results indicate that the previously observed increase of whole-stream NO₃^– uptake in agricultural streams is attributable to nutrients and light stimulating benthic uptake, while fine sediment effects and the role of the hyporheic compartment to total uptake are modest. Moreover, the finding that stressor interactions vary with ecosystem compartments calls for a consideration of all compartments and their contribution to whole-system functioning in multiple stressor studies. We are beginning to understand how multiple interacting stressors affect stream functioning, but more mechanistic evidence is needed to disentangle whether additive or non-additive effects prevail in human-altered ecosystems.