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Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment. The authors acknowledge COST Action ES 1105 “CYANOCOST – Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management” and COST Action ES 1201 “NETLAKE – Networking Lake Observatories in Europe” for contributing to this study through networking and knowledge sharing with European experts in the field. Evanthia Mantzouki was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation (SERI) to Bas Ibelings and by supplementary funding from University of Geneva. We thank Wendy Beekman for the nutrient analysis and the University of Wageningen for covering the costs of this analysis from the personal funding of dr. Miquel Lürling. We thank Pieter Slot for assisting with the pigment analysis and the University of Amsterdam for covering the costs of the analysis through funding from the group of Prof. Jef Huisman and dr. Petra Visser (IBED). We would like to thank the Environmental Data Initiative for covering the cost of archiving the EMLS dataset. We would like to thank the Leibniz Institute of Freshwater Ecology and Inland Fisheries, Dept. of Experimental Limnology and the Aquatic Microbial Ecology Group for logistic and technical support of J. Fonvielle and H.-P. Grossart; and the Leibniz Association for financial support. The collection of data for Lough Erne and Lough Neagh were funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland. The authors acknowledge COST Action ES 1105 “CYANOCOST – Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management” and COST Action ES 1201 “NETLAKE – Networking Lake Observatories in Europe” for contributing to this study through networking and knowledge sharing with European experts in the field. Evanthia Mantzouki was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation (SERI) to Bas Ibelings and by supplementary funding from University of Geneva. We thank Wendy Beekman for the nutrient analysis and the University of Wageningen for covering the costs of this analysis from the personal funding of dr. Miquel Lürling. We thank Pieter Slot for assisting with the pigment analysis and the University of Amsterdam for covering the costs of the analysis through funding from the group of Prof. Jef Huisman and dr. Petra Visser (IBED). We would like to thank the Environmental Data Initiative for covering the cost of archiving the EMLS dataset. We would like to thank the Leibniz Institute of Freshwater Ecology and Inland Fisheries, Dept. of Experimental Limnology and the Aquatic Microbial Ecology Group for logistic and technical support of J. Fonvielle and H.-P. Grossart; and the Leibniz Association for financial support. The collection of data for Lough Erne and Lough Neagh were funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland.