Abstract:The distribution patterns of surface sediment diatom assemblages from 49 lakes were used to explore the relationship between limnological variables and diatom assemblages as well as to assess an ecological classifi cation system as a tool for the management and conservation of Icelandic freshwaters. Lakes were limnologically diverse ranging from deep, oligotrophic, ionically dilute lakes, to shallow lakes with a wide range of nutrient and ionic contents. Physical conditions (depth, surface area, surface water temperature) and nutrient and ion concentrations differed signifi cantly among ecological lake categories (i.e., plateau, spring-fed, direct-runoff, valley, glacial, and coastal lakes) (ANOVA, p < 0.05). Diatom assemblages were taxonomically diverse (329 taxa) with strong representation of planktonic, benthic and periphytic forms. Small benthic Fragilaria sensu lato (19 species and varieties) were the most abundant with combined abundances > 20 % in all but 4 of the lakes, most likely due to the generally cold lake water conditions in this subarctic region. Variation in diatom distributions was best explained by the combination of mean depth (infl uencing littoral versus planktonic habitats), surface water temperature, specifi c conductivity, alkalinity, total organic carbon, total nitrogen and SiO 2 in a canonical correspondence analysis (CCA). However, these variables did not explain distribution patterns amongst small benthic Fragilaria taxa, although some weak relationships between some taxa and these variables were evident. Distinct diatom assemblages and limnological properties among ecological lake categories support the classifi cation of Icelandic freshwaters based on major topographic, geological and hydrological characteristics. More detailed inclusion of lake depth along with lake basin form, as well as more refi ned categories of lake water origin and topographical positioning to better approximate regional climatic conditions, may improve the ecological classifi cation of Icelandic freshwaters for conservation and management practices.