Here, we present data that for the first time suggests that the effects of atmospheric nitrogen (N) deposition on nutrient limitation extend into the food web. We used a novel and sensitive assay for an enzyme that is over-expressed in animals growing under dietary phosphorus (P) deficiency (alkaline phosphatase activity, APA) to assess the nutritional status of major crustacean zooplankton taxa in lakes across a gradient of atmospheric N deposition in Norway. Lakes receiving high N deposition had suspended organic matter (seston) with significantly elevated carbon:P and N:P ratios, indicative of amplified phytoplankton P limitation. This P limitation appeared to be transferred up the food chain, as the cosmopolitan seston-feeding zooplankton taxa Daphnia and Holopedium had significantly increased APA. These results indicate that N deposition can impair the efficiency of trophic interactions by accentuating stoichiometric food quality constraints in lake food webs.