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High mountain lakes are a network of sentinels, sensitive to any events occurring within their waterbodies, their surrounding catchment and their airshed. In this paper, we investigate how catchments impact the taxonomic and functional composition of phytoplankton communities in high mountain lakes, and how this impact varies according to the atmospheric nutrient deposition regime. For two years, we sampled the post snow-melt and the late summer phytoplankton, with a set of biotic and abiotic parameters, in six French alpine lakes with differing catchments (size and vegetation cover) and contrasting nitrogen (N) and phosphorus (P) deposition regimes. Whatever the nutrient deposition regime, we found that the lakes with the smallest rocky catchments showed the lowest functional richness of phytoplankton communities. The lakes with larger vegetated catchments were characterized by the coexistence of phytoplankton taxa with more diverse strategies in the acquisition and utilization of nutrient resources. The nutrient deposition regime appeared to interact with catchment characteristics in determining which functional groups ultimately developed in lakes. Photoautotroph taxa dominated the phytoplankton assemblages under high NP deposition regime while mixotroph taxa were even more favored in lakes with large vegetated catchments under low NP deposition regime. Phytoplankton functional changes were likely related to the leaching of terrestrial organic matter from catchments evidenced by analyses of carbon (delta C-13) and nitrogen (delta N-15) stable isotope ratios in seston and zooplankton. Plankton delta N-15 values indicated greater water-soil interaction in lakes with larger vegetated catchments, while delta C-13 values indicated the effective mineralization of the organic matter in lakes. The role played by catchments should be considered when seeking to determine the vulnerability of high altitude lakes to future changes, as catchments' own properties will vary under changes related to climate and airborne contaminants. (C) 2019 Elsevier B.V. All rights reserved.