We present a methodology to develop the integrated toxicity and climate change risk assessment of Europe based facilities, industries and regions. There is an increasingly important need for large scale sustainability measurement solutions for company reporting with high granularity. In this paper we measure key aspects of Sustainable Development Goals in terms of human, cancer and non-cancer toxicity, ecotoxicity together with global warming impact potentials from point source pollutant releases of more than 10,000 companies and their 33,000 facilities in Europe from 2001 to 2017, by using the European Pollutant Release and Transfer Register. For our assessment, we deploy a scientific consensus model, USEtox for characterizing human and ecotoxicological impacts of chemicals and the global warming potential values from the Intergovernmental Panel on Climate Change. We discuss water and air emissions of dozens of pollutants in urban, rural, coastal and inland areas. Companies in the electricity production sector are estimated to have the largest human toxicity impact potential (46% of total) and the largest global warming impact potential (50%), while companies in the sewerage sector have the largest ecotoxicity impact potential (50%). In the overall economy, the correlation between facilities’ global warming and toxicity impact potentials is positive, however, not very strong. Therefore, we argue that carbon footprint of industrial organizations can be only used as a climate change risk indicator, but not as an overall environmental performance indicator. We confirm impact potentials of major pollutants in previous research papers (Hg accounting for 76% of the total human toxicity and Zn accounting for 68% of total ecotoxicity), although we draw the attention to the limitations of USEtox in case of metals. From 2001 to 2017 total human toxicity dropped by 28%, although the downward trend reversed in 2016. Ecotoxicity and global warming impact potentials remained unchanged in the same period. Finally, we show that the European pollutant release monitoring data quality could be further improved, as only three quarters of the toxic releases are measured in the Member States of the European Union, and a high share of toxic pollutant releases are only estimated in some countries. Of the measured or calculated toxic releases, only one third is reported according to the most robust CEN/ISO standards and about one fifth according to the least preferred other methods, like engineering judgements.