During the last decades, atmospheric nitrogen loading in mountain ranges of the Northern Hemisphere has increased substantially, resulting in high nitrate concentrations in many lakes. Yet, how increased nitrogen has affected denitrification, a key process for nitrogen removal, is poorly understood. We measured actual and potential (nitrate and carbon amended) denitrification rates in sediments of several lake types and habitats in the Pyrenees during the ice-free season. Actual denitrification rates ranged from 0 to 9 μmol N 2 O m −2 h −1 (mean, 1.5 ± 1.6 SD), whereas potential rates were about 10times higher. The highest actual rates occurred in warmer sediments with more nitrate available in the overlying water. Consequently, littoral habitats showed, on average, 3-fold higher rates than the deep zone. The highest denitrification potentials were found in more productive lakes located at relatively low altitude and small catchments, with warmer sediments, high relative abundance of denitrification nitrite reductase genes, and sulphate-rich waters. We conclude that increased nitrogen deposition has resulted in elevated denitrification rates, but not sufficiently to compensate for the atmospheric nitrogen loading in most of the highly oligotrophic lakes. However, there is potential for high rates, especially in the more productive lakes and landscape features largely govern this. Reactive nitrogen (N r) in the environment has at least doubled since preindustrial times due to human activities 1. This anthropogenic alteration is one of the critical problems facing Earth-system processes 2 , as N r can cause multiple effects across ecosystems until it is transformed back to nonreactive N 2 3 by denitrification 4,5. This microbial process reduces nitrogenous oxides, mainly nitrate and nitrite, to dinitrogen gases N 2 O and N 2 which are emitted to the atmosphere 6. Freshwater ecosystems account for about 20% of global denitrification, and being hot spots for denitrification, they exceed the activity of soils per unit area on an annual basis 4. Many mountain areas of the Northern Hemisphere have received large atmospheric loadings of N r during the last decades 7-10 , resulting in elevated nitrate concentrations in mountain streams and lakes 7. These waters are deficient in phosphorus (P), and therefore the supply of N usually exceeds the assimilation capacity by algae 7. Thus, phytoplankton and benthic algae growth is P limited in mountain lakes affected by high N deposition 7,11. Despite that N deposition can be homogeneous throughout a region 12 , nitrate accumulation in the lakes differs depending on internal and external P loads. In more productive lakes, the accumulation of organic C and N in the sediments is higher and nitrate remaining in the water column lower. Small lakes usually show higher productivity, particularly, if they are located at lower altitude as the growing season is longer and nutrient and organic matter (OM) loads from the surroundings increases 13,14. While nitrate accumulation in mountain l...