In the Alps, as in other mountainous regions across the world, nitrogen (N) enrichment of ecosystems via atmospheric deposition is a major environmental concern. Nitrogen enrichment can cause acidification in poorly buffered lakes and streams, but here we assessed the less well-known effects of eutrophication on the phytobenthos of lakes and its consequences for grazing. To simulate the effects of N deposition, we conducted experimental nutrient additions (N and N+P) in two lakes in the French Alps, in summer 2012. In each lake, we deployed nutrient-diffusing substrata for 22 days. The substrata were placed within cages that either allowed or prevented access by macrograzers. We tested the hypotheses that N enrichment: (i) increases phytobenthic biomass, (ii) alters phytobenthic taxonomic composition and (iii) reduces benthic grazing. Supporting the first hypothesis, at the end of the experiments N-enriched substrata had a greater phytobenthic biomass than unenriched substrata, indicating N limitation. Supporting the second hypothesis, the taxonomic composition of the phytobenthos differed between N-enriched and control substrata. Green algae, including filamentous forms, were favoured by N enrichment to a greater extent than diatoms and cyanobacteria. By contrast, the third hypothesis was not supported. Grazing had the same effect on the biomass of the phytobenthos regardless of nutrient treatment. Our results highlight the sensitivity of Alpine lakes to deposition of atmospheric N. Its ecological effects are not limited to acidification, but also include increased biomass (eutrophication) and altered taxonomic composition of the phytobenthos. Because filamentous green algae favoured by N enrichment are usually unpalatable to macrograzers, inputs of atmospheric N could reduce the efficiency of transfer of energy from the phytobenthos up through the food web.