Air pollution has significantly increased during the Anthropocene, adversely affecting ecosystems and human health. The National Emission Ceilings Directive (NECD, 2016/2284/EU) set targets for reducing emissions and required Member States to establish a national monitoring network to assess ecosystem changes due to air pollution. For freshwaters, the NECD monitoring focused on assessing effects of sulphur and nitrogen deposition and acidification status using chemical parameters and sensitive biological indicators. This paper evaluates the present NECD monitoring scheme and its applicability in Italy, from site selection to initial data collection. High mountain lakes were selected as study sites, because they are free from direct human impacts and sensitive to air pollutant deposition. A two-year survey of chemical and biological components (diatoms and macroinvertebrates) was conducted in eight lakes with the aim to (1) assess the suitability of chemical parameters and biological indices for evaluating air pollutant impacts on sensitive water bodies in Italy, focusing on acidification and nitrogen enrichment, and (2) discuss the current approach's achievements and limitations. Results highlighted the need to develop specific indices for detecting atmospheric pollution impacts on freshwater ecosystems. Beside acidification, other drivers, including nutrients, proved to be important in shaping mountain lakes biological assemblages and affecting their response to pollutant deposition. Our study contributed to a critical assessment of the present freshwater monitoring under the NECD from the Italian perspective, providing indications on future improvement and development of the monitoring scheme itself.