Diatoms were identified and enumerated from the surface sediments of 65 lakes located on the Cariboo and Chilcotin Plateaux (British Columbia, Canada). These lakes span a large gradient in lakewater ionic concentration (fresh through hypersaline) and composition, as well as other physical/chemical variables. Almost all of the study lakes had higher salinities in the late-summer than in the spring. The lakes with spring salinities > 8 gl(-1) showed the largest seasonal increases in salinity. Ionic composition was similar in the spring and late-summer for most lakes. Both ionic concentration (i.e. salinity) and composition were important environmental variables that could account for the different diatom floras in the lakes. Diatom assemblages characteristic of carbonate-dominated and sulfate-dominated waters were identified. Other variables such as water depth and phosphorus concentration were also important. The majority (87%) of diatom taxa had estimated salinity optima < 3 gl(-1). Halophilic diatom taxa had broader tolerances to salinity when compared to the fresh water taxa, however taxa with narrow and broad tolerances could be identified across the salinity gradient. Species diversity was weakly but significantly correlated to lakewater salinity (r(2) = 0.18 to 0.3, P < 0.05). Salinity inference models were developed based on the relationship between the diatom assemblages and the spring, late-summer and average salinity. The correlations between the measured and diatom-inferred salinity, based on the spring (r = 0.95), late-summer (r = 0.94) and average (r = 0.95) salinity data, are high because there was an extremely strong correlation (r = 0.98) between the log transformed spring and late-summer measured salinities. These salinity reconstruction models provide a tool that can be used to infer past climatic changes as part of paleolimnological studies from appropriate closed-basin lakes in British Columbia.