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Diatom profiles in closed-basin lake sediments are commonly used to reconstruct climate change based on the observed correlations between salinity (ionic concentration) and modern diatom assemblages. Diatom assemblages are strongly correlated not only with salinity but also anion composition, with certain taxa characteristic of carbonate systems and others sulfate-dominated waters. Although strong correlations exist, the actual mechanisms behind these correlations are unknown. Here we briefly review the influence of salinity and ionic composition on nutrient dynamics in saline lakes and suggest that these interactions may drive shifts in diatom species composition along gradients of ionic concentration/ composition. We discuss the influence of salinity and anion composition on nutrient availability, as well as on nutrient requirements and uptake by diatoms.