1. Mountain lake sediments are valuable archives of environmental change. However, the presence of multiple drivers of change over similar or overlapping timescales may obscure palaeolimnological signals obtained using traditional statistical analyses. 2. As part of the European Union-funded EMERGE programme, sediment cores were obtained from 209 mountain lakes across 11 lake districts spanning gradients of altitude, latitude, geochemistry and atmospheric deposition. Surface sediments (0-0.5 cm) were subsampled to represent modern conditions corresponding with chemical and environmental measurements, while core bottom (15-17 cm) sediments were subsampled to represent the pre-industrial period. 3. We used a novel approach to explore the relative importance of environmental drivers of change in diatom communities. First, we used canonical correspondence analysis (CCA) to identify the most significant variables explaining diatom community distributions in lake surface sediments. Lake water pH, nitrate concentration ⁄ dissolved organic carbon (DOC) and ice-free period were identified as uniquely significant explanatory variables along three primary axes of variation. The modern data set was then used to construct transfer functions linking diatom communities to these key variables. We applied these transfer functions to core bottom samples to reconstruct change since the pre-industrial period. 4. Drivers of diatom community change differed among regions. Diatom-inferred pH declined in five acid-sensitive lake districts (Central & Southern Norway, Piedmont Ticino, Retezat Mountains, Scotland and Tatra Mountains), consistent with acidification caused by sulphur and nitrogen deposition. Diatom-inferred pH increased in two lake districts [Julian Alps (JA), Pyrenees (PY)], probably due to eutrophication and climate warming-induced increases in weathering rates respectively. 5. Diatom inference models for nitrate and DOC were not independent. However, diatom-inferred nitrate increased in all lake districts with detectable changes, except for the Retezat Mountains. These changes are consistent with increased nitrogen deposition and leaching in the industrial period and are independent of acidification effects, presumably reflecting a nitrogen fertilization effect. Diatom-inferred DOC increased in the Correspondence: C. J. Curtis, Environmental