Nutrient enrichment experiments were conducted in 1.2-m deep enclosures in 2 shallow, oligotrophic, mountain lakes. ¹⁵N-NO₃ isotope tracer was used to compare the importance of phytoplankton and benthic compartments (epilithon, surface sediment [epipelon], and subsurface sediment) for NO₃ uptake under high and low NO₃ conditions. NO₃ uptake approached saturation in the high-N lake, but not in the low-N lake. The capacity of phytoplankton and benthic compartments to take up NO₃ differed among treatments and between lakes, and depended on water-column nutrient conditions and the history of NO₃ availability. Phytoplankton productivity responded strongly to addition of limiting nutrients, and NO₃ uptake was related to phytoplankton biomass and photosynthesis. However, more NO₃ usually was taken up by benthic compartments (57–92% combined) than by phytoplankton, even though the response of benthic algal biomass to nutrient additions was less pronounced than that of phytoplankton and benthic NO₃ uptake was unrelated to benthic algal biomass. In the low-N lake where NO₃ uptake was unsaturated, C content or % was related to NO₃ uptake in benthic substrates, suggesting that heterotrophic bacterial processes could be important in benthic NO₃ uptake. These results suggest that phytoplankton are most sensitive to nutrient additions, but benthic processes are important for NO₃ uptake in shallow, oligotrophic lakes.