As part of a comprehensive evaluation of the status of remote mountain lake ecosystems throughout Europe, the response of key organisms in mountain lakes to variations in environmental gradients due to geography and climate, pollution and catchment characteristics was evaluated. Samples were taken from the pelagic (zooplankton, bacteria and chlorophyll a) and littoral (benthic invertebrates and epilithic diatoms) zones. Surface sediment core sub-samples were taken for analysis of sub-fossil cladocera, chironomids, diatoms and pigments. Concentrations of trace metals, persistent organic pollutants and spheroidal carbonaceous particles were also measured. This paper describes the variation in species composition and environmental characteristics of upland lochs across northern Scotland and examines how the former may be related to the latter. Multivariate techniques were employed to examine patterns and relationships within and among the multivariate species and environmental datasets. Results show that in remote mountain lakes in Scotland, biological assemblages of key organisms groups are driven by a number of environmental gradients, in particular organic content and acid-base status. It appears that these systems can broadly be divided, on the basis of their species composition into two main types. Low alkalinity lochs with sparse soil coverage at higher altitudes have distinctly different biological communities compared with lochs with high organic levels and high proportions of peaty soils in the catchments