Summary1. A survey of c. 350 remote high altitude and high latitude lakes from 11 different mountain regions was undertaken to explore species distribution across Europe at a scale not previously attempted.2. Lakes were sampled for planktonic crustaceans, rotifers, littoral invertebrates and sub‐fossil chironomids, diatoms and cladocerans. Each lake was characterised in terms of water chemistry, morphology, catchment attributes and geographical location.3. Separate twinspan analyses were undertaken on diatom, chironomid, planktonic crustacean, littoral invertebrate and cladoceran (chydorids only) data to classify sites according to taxonomic composition. For most datasets there was a spatial component to the classification with distinct geographical groups emerging – Norway and Scotland, Finland and Central/Eastern Europe.4. Constrained ordination methods were employed to examine how species responded to a range of environmental factors, which were aggregated into a series of component groups – proximal environment (the chemical, trophic and physical attributes of the lake), catchment characteristics and geographical location. Several key environmental gradients were identified, which explained significant levels of the variance across several of the biological groups including dissolved organic carbon (chironomids, planktonic crustaceans), temperature (chironomids and littoral invertebrates), chloride/sea‐salt (littoral invertebrates, diatoms and rotifers), lake morphology (all groups), calcium/pH (diatoms), nitrate (chydorids, littoral invertebrates, rotifers and planktonic crustaceans) and fish (littoral invertebrates). In some cases these statistical relationships are likely to represent direct ecological constraints and, in others, it is probable that the environmental variable is acting as a surrogate for some other attribute or process.5. Variance partitioning was undertaken to quantify how much of the variation in each biological group could be uniquely attributed to variables representing the proximal environment, catchment characteristics and geographical location. For most groups the location of the lake tends to explain the greatest variation in species composition across the Lake Districts. The proximal environment was also important but, with the exception of diatoms, secondary to location. Therefore, a strong geographical signal emerged from the analyses. Three distinct limno‐regions were identified; Nordic (Scotland and Norway), Sub‐Arctic (Northern Finland) and Alpine (Pyrenees, the Alps and Eastern Europe ranges).6. Our results have implications for the development of regionalisation schemes based on biological responses to environmental gradients; (i) lake ‘types’ based on environmental factors cannot be extrapolated throughout Europe, even within the relatively narrow gradients found in remote mountain lakes, (ii) biotic response to large‐scale variations in environmental conditions, such as those that could be expected with climate change, is likely to vary according to regions because of the biogeographical differences among them.